Therapeutic indazoles

ABSTRACT

The invention provides compounds of formula I: 
     
       
         
         
             
             
         
       
     
     and salts thereof wherein R 1 -R 5  have any of the meanings described in the specification. The compounds are useful for treating bacterial infections (e.g. tuberculosis).

PRIORITY

This application is a Divisional of U.S. application Ser. No.16/642,817, which is a 35 U.S.C. § 371 application of InternationalApplication No. PCT/2018/048611, filed on Aug. 29, 2018, which claimsbenefit of priority to U.S. Provisional Application No. 62/551,534,filed Aug. 29, 2017. The entire content of these applications isincorporated herein by reference.

GOVERNMENT FUNDING

This invention was made with government support under 1U19Al109713,R21Al111647, and R33Al11167 awarded by the National Institutes ofHealth. The government has certain rights in the invention.

BACKGROUND

Tuberculosis (TB) is an ongoing global health threat, made worse by anincrease in drug-resistant Mycobacterium tuberculosis (TB) (Lin, J., etal., Int J Tuberc Lung Dis, 2004, 8, 568-573). The development of new TBdrugs has not kept pace with drug-resistance. Clinical drug-resistancehas been identified among even the most recently approved drugsbedaquiline (BDQ) and delamanid (Bloemberg, G. V., et al., Engl J Med,2015, 373, 1986-1988), prompting concerns that TB may becomeuntreatable. TB regimens require lengthy treatment—six months for drugsusceptible TB and >18 months for drug-resistance TB. A lengthytreatment duration provides ample opportunity for partial non-compliancethat can lead to both treatment failure and the emergence of newdrug-resistance (Gelmanova, I. Y., et al., Bull World Health Oran, 2007,85, 703-711; Pablos-Mendez, A., et al., Am J Med, 1997, 102, 164-170;and Saunders, N.J., et al., J Infect, 2011, 62, 212-217). Thus, new TBtherapies are needed to both counter emerging drug-resistance and toenable shortened TB treatments (Global tuberculosis report 2016 (Geneva:World Health Organization)).

Renewed efforts to find new anti-TB leads have led to the discovery ofthousands of whole cell active compounds and novel chemotypes. Many ofthese compounds are undergoing optimization to deliver a lead forfurther drug development (Ananthan, S et al., Tuberculosis (Edinb),2009, 89, 334-353; Ballell, L., et al., Chem Med Chem, 2013, 8, 313-321;and Maddry, J. A., et al., Tuberculosis (Edinb), 2009, 89, 354-363). Thecell-wall is well established to be one of the most vulnerablesubcellular components of bacteria including M. tuberculosis. Inhibitorsof cell-wall biosynthesis disrupt the outer cell-envelope causing rapidcell death, and a number of drugs that target the cell-wall such asisoniazid (INH), ethambutol (EMB), ethionamide (ETH), carbapenems anddelamanid are effective at treating clinical TB. Furthermore, many ofthe enzymes involved in biosynthesis of the M. tuberculosis cell-wall donot have close homologues in humans, suggesting that specific inhibitorsof this pathway would be less toxic. A screen for selecting cell-wallspecific anti-tuberculars using a whole-cell reporter that signaledtranscriptional induction of the iniBAC operon that is specificallyinduced by cell-wall inhibitors has previously been described (Alland,D., J Bacteriol, 2000, 182, 1802-1811). This screen led to the discoveryof the thiophenes as inhibitors of polyketide synthase 13 (Pks13)(Wilson et al., 2013) and DAS/DA8 that inhibited MmpL3 (Tahlan, K., etal., Antimicrob Agents Chemother, 2012, 56, 1797-1809).

The mycobacterial cell-wall is adorned with essential mycolic acids,which are synthesized by a fatty acid synthase-1l (FAS-II) system thatis absent in humans. The FAS-II complex consists of five enzymes encodedin two operons: one operon encoding three enzymes β-ketoacyl-ACPsynthases KasA and KasB, an acyl-carrier protein (AcpM) and the secondoperon encoding the ketoreductase (MabA) and the enoyl reductase(InhA)(Banerjee, A., et al., Science, 1994, 263, 227-230; and Banerjee,A., et al., Microbiology, 1998, 144 (Pt 10), 2697-2704). This complexcarries out cyclic elongation of short-chain fatty acids to producelong-chain meromycolic acids (C₄₈-C₆₈) (Bhatt, A., et al., J Bacteriol,2005, 187, 7596-7606) that are condensed with C26 fatty acids to yieldbranched mycolic acids by Pks13 (Portevin, D., et al., Proc Natl AcadSci USA, 2004, 101, 314-319; and Wilson, R., et al., Nat Chem Biol,2013, 9, 499-506). Mycolic acid variants are not only critical forpathogenesis, virulence, and persistence (Bhatt, A., et al., MolMicrobiol, 2007, 64, 1442-1454; Dubnau, E., et al., Mol Microbiol, 2000,36, 630-637; and Glickman, M. S., et al., Mol Cell, 2000, 5, 717-727),but they are also effective targets for anti-TB drugs. For example, INH,one of the most effective first-line anti-tubercular drugs, targetsInhA. KasA has also been shown to be essential and a vulnerable targetin mycobacteria (Bhatt, A., et al., Mol Microbiol, 2007, 64, 1442-1454).Unfortunately, previously known inhibitors of KasA/KasB, thiolactomycin(TLM) (Kapilashrami, K., et al., J Biol Chem, 2013, 288, 6045-6052; Lee,W., et al., Biochemistry, 2011, 50, 5743-5756; Machutta, C. A., et al.,J Biol Chem, 2010, 285, 6161-6169; and Schiebel, J., et al., J Biol Chem2013, 288, 34190-34204) and platensimycin (Brown, A. K., et al., PoSOne, 2009, 4, e6306) have very poor whole-cell activity in M.tuberculosis of 142 and 27 μM, respectively.

Currently there is a need for agents and methods that are useful fortreating bacterial infections such as tuberculosis.

SUMMARY

Small molecule indazole sulfonamides have been synthesized anddemonstrated to be potent inhibitors of Mycobacterium tuberculosis inculture and more specifically to be inhibitors of the M. tuberculosisenzyme KasA. Representative molecules in these classes exhibitacceptable physiochemical, in vitro ADME, and mouse PK profiles. Selectmolecules have been crystallized with KasA and their binding modes tothe target protein have been elucidated. Select molecules have exhibitedin vivo activity in a mouse model of acute M. tuberculosis infection.DG167 has also exhibited in vivo synergy with isoniazid in a mouse modelof acute M. tuberculosis infection.

Accordingly, in one embodiment the invention provides a compound offormula I:

or a salt thereof, wherein:

R¹ is H, (C₁-C₄)alkyl, phenyl, or benzyl;

R² is H, halo, or (C₁-C₄)alkyl that is optionally substituted with oneor more halo;

R³ is H and R⁴ is —N(R^(a))SO₂R^(c), —N(R^(a))C(═S)N(R^(a))R^(c),—N(R^(a))C(═O)R_(c), —N(R^(a))C(═O)OR^(c), —N(R^(a))R^(d), or—N(R^(a))C(═O)N(R^(a))R^(c); or R³ is —N(R^(a))SO₂R^(c),—N(R^(a))C(═S)N(R^(a))R^(c), —N(R^(a))C(═O)R^(c), —N(R^(a))C(═O)OR^(c),—N(R^(a))R^(d), or —N(R^(a))C(═O)N(R^(a))R^(c) and R⁴ is H;

R⁵ is H, (C₁-C₄)alkyl, or halo;

each R^(a) is independently H or (C₁-C₄)alkyl;

R^(c) is (C₃-C₆)cycloalkyl, piperidinyl, or (C₂-C₆)alkyl, wherein any(C₃-C₆)cycloalkyl and (C₂-C₆)alkyl is optionally substituted with one ormore groups independently selected from the group consisting of halo,(C₃-C₆)cycloalkyl, phenyl, (C₁-C₄)alkoxy, trifluoromethyl, and cyano;and

R^(d) is (C₃-C₆)cycloalkyl, or (C₂-C₆)alkyl, wherein any(C₃-C₆)cycloalkyl and (C₂-C₆)alkyl is optionally substituted with one ormore groups independently selected from the group consisting of halo,(C₃-C₆)cycloalkyl, phenyl, (C₁-C₄)alkoxy, trifluoromethyl, and cyano;

provided the compound is not:

The invention also provides a pharmaceutical composition comprising acompound of formula I or a pharmaceutically acceptable salt thereof, anda pharmaceutically acceptable excipient.

The invention also provides a method for treating a bacterial infectionin an animal (e.g., a mammal such as a human) comprising administering acompound of formula I or a pharmaceutically acceptable salt thereof tothe animal.

The invention also provides a compound of formula I or apharmaceutically acceptable salt thereof for use in medical therapy.

The invention also provides a compound of formula I or apharmaceutically acceptable salt thereof for the prophylactic ortherapeutic treatment of a bacterial infection.

The invention also provides the use of a compound of formula I or apharmaceutically acceptable salt thereof to prepare a medicament fortreating a bacterial infection in an animal (e.g. a mammal such as ahuman).

The invention also provides processes and intermediates disclosed hereinthat are useful for preparing a compound of formula I or a salt thereof.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 Shows Table 1, DG167 active in laboratory and clinical strains ofM. tuberculosis (Mtb).

FIG. 2 Shows Table 2, genotypic and drug-resistance profile (MIC in μM)of DG167 resistant Mtb isolates

FIG. 3 Shows Table 3, structure-Activity Relationships forRepresentative Compounds.

FIGS. 4A-4D DG167 inhibits mycolic acid biosynthesis in vivo. (FIGS.4C-4D) Normal-phase TLC analysis of MAMEs/FAMEs from wild-type M.tuberculosis (H37Rv) and the DG167-resistant M. tuberculosis (isolate:DRM167-32x2, Table 1). The cultures were treated with increasingconcentrations of DG167 and inactive analog 5a-2. Total lipids wereextracted, methyl esterified post ¹⁴C-acetate incorporation and resolvedby TLCs (FIG. 4A) M. tuberculosis H37Rv (FIG. 4B). M. tuberculosisDRM167-32x2 isolate. (FIG. 4C) Densitometric analysis of MAMEs and FAMEsfrom panel A using ImageQuant (GE Healthcare) (FIG. 4D). Densitometricanalysis of MAMEs and FAMEs from panel B. Equal counts (20,000 cpm) wereloaded and the TLC was developed using hexane/ethyl acetate (19:1, v/v,2 runs).

FIGS. 5A-5C DG167 synergizes with INH in vitro and in vivo. (FIG. 5A) Invitro killing curves for the M. tuberculosis strain H37Rv afterincubation with given concentrations of DG167, INH, or a combination ofthese drugs. Killing activity was monitored by plating for CFUs; (FIG.5B) Venn diagram showing differential gene expression from an RNAseqexperiment upon treatment with 10× DG167, 10×INH or the drugcombination: (FIG. 5C) In vivo efficacy of DG167 and INH alone and incombination in an acute model of M. tuberculosis infection in mice. Thearrow indicates the day when treatment was started.

FIGS. 6A-6C Schematic representation of (FIG. 6A) DG167_(A)-DG167_(B),and DG167_(A)-KasA interactions, (FIG. 6B) DG167_(A)-DG167_(B),DG167_(B)-KasA, and DG167_(B)-KasA′ interactions, and (FIG. 6C) KasA-PLinteractions in PDB ID 4C72 chain A (Schiebel, J., et al., J Biol Chem,2013, 288, 34190-34204). Molecules are labeled consistently throughoutthe figure—DG167_(A) is depicted as green bonds, DG167_(B) is depictedas magenta bonds, phospholipid (PL) is depicted as yellow bonds, andhydrogen bonds are depicted as dashed lines measured in Å. In panel A,the blue semicircles with radiating lines represent hydrophobic contactsmediated by KasA residues and DG167_(A). In panel B, the bluesemicircles with radiating lines represent hydrophobic contacts mediatedby KasA residues and DG167_(B), while orange semicircles with radiatinglines represent hydrophobic contacts mediated by KasA′ residues andDG167_(B). In panel C, the blue semicircles with radiating linesrepresent hydrophobic contacts mediated by KasA residues and PL, whileorange semicircles with radiating lines represent hydrophobic contactsmediated by KasA′ residues and PL. PL-binding residues surrounded with agreen, magenta, or red line identify residues from the KasA-DG167structure that interact with DG167_(A), DG167_(B), or both,respectively. The schematic was produced with LIGPLOT (Wallace, A. C.,et al., Protein Eng. 1995, 8, 127-134).

FIG. 7 Synthetic scheme. The N-methylation of commercially available6-nitro-1H-indazole afforded a mixture of 1-methyl-6-nitro-1H-indazoleand 2-methyl-6-nitro-1H-indazole. The chromatographically separable1-methyl-6-nitro-1H-indazole was reduced and then the free amine wasderivatized using four different methods depending on the desiredfunctional group to generate the analytically pure compounds. The parentcompound (DG167) was synthesized by treating6-amino-1-methyl-1H-indazole with butane-1-sulfonyl chloride in thepresence of pyridine. Reagents and conditions: (a)(i) NaH, DMF, 0° C.,30 min (ii) R¹I, DMF, room temperature, 16 hours or R¹I (1.2 eq), CuI(0.05 eq), K₃PO₄ (2 eq), N,N-dimethylethylenediamine (0.1 eq), DMF, 110°C., 72 hours; (b) 10 wt % Pd/C, HCOONH₄, EtOH, room temperature, 4hours; (c) R²SO₂Cl, py, room temperature, 16 hours; (d) (i) NaH, DMF, 0°C., 30 min (ii) CH₃I, DMF, room temperature, 16 hours; (e) R²NCS/R²CNO,TEA, DCM, 40° C., 16 hours; (f) (i) 1,1′ carbonyldiimidazcole, DCM, 35°C. 4 hours; (ii) R²OH, DCM, 35° C., 16 h; (g) R²COCl, py, roomtemperature, 16 hours; (h) LiAlH₄, THF, 4 hours.

FIG. 8 Oral Bioavailability of DG167. DG167 was orally bioavailable anddotted line showed exposure in plasma above the MIC (104 ng/ml=0.39 μM).The mice dosing was either oral (PO 25 mg/kg) or intravenous (IV 5mg/kg) in the following formulations and DG167 levels were measured inplasma using LC/MS. Each point was the average of three replicates. POstudy in mice (25 mg/kg); 0.5% CMC/0.5% Tween 80; AUC [0-t]=8083.96h*ng/mL; Bioavailability (%)=92.3; IV study in mice (5 mg/kg): 5%DMA/40% PEG300/55% D5W; AUC [0-t]=1751.25 h*ng/mL; t/2=0.33 h.

FIG. 9 shows data for DG167 Tolerability Study with combined dosing ofDG167 (100 mg/kg) and INH (25 mg/kg).

FIG. 10 shows the reduction of M. tuberculosis colony-forming units inthe lungs of infected mice (PMID: 25421483) treated with compound 43 ascompared to INH treatment and vehicle only.

FIG. 11 shows the kinetic solubility and in vitro metabolic stability ofthe compounds of Examples 41, 42, 43, and 45. Published protocols wereutilized to determine mouse and human liver microsomal stability (PMID:26257441) and kinetic solubility (Kerns. E. H.; Di, L. Drug-likeProperties: Concepts, Structure Design and Methods: from ADME toToxicity Optimization; Elsevier: Amsterdam, 2008.)

FIG. 12 illustrates the synthesis of representative compounds of theinvention.

FIGS. 13A-13G show pharmacokinetic profiles of (FIG. 13A) Example 41,(FIG. 13B) Example 43, (FIG. 13C) Example 42, (FIG. 13D) Example 45,(FIG. 13E) Example 44, (FIG. 13F) Example 48, and (FIG. 13G) Example 46in CD-1 female mice dosed at 25 mg/kg po. The dashed line in each plotrepresents the MIC of each compound. A published protocol was utilizedfor the mouse PK studies (PMID: 29311070).

FIGS. 14A-14B show the pharmacokinetic profiles of (FIG. 14A) Example 43and (FIG. 14B) Example 43 from a single dose of 5 mg/kg iv and 25 mg/kgpo. A published protocol was utilized for the mouse PK studies (PMID:29311070).

DETAILED DESCRIPTION

The following definitions are used, unless otherwise described: halo orhalogen is fluoro, chloro, bromo, or iodo. Alkyl, alkoxy, etc. denoteboth straight and branched groups; but reference to an individualradical such as propyl embraces only the straight chain radical, abranched chain isomer such as isopropyl being specifically referred to.

The term “alkyl”, by itself or as part of another substituent, means,unless otherwise stated, a straight or branched chain hydrocarbonradical, having the number of carbon atoms designated (i.e., C₁₋₈ meansone to eight carbons). Examples include (C₁-C₈)alkyl, (C₂-C₈)alkyl,C₁-C₆)alkyl, (C₂-C₆)alkyl and (C₃-C₆)alkyl. Examples of alkyl groupsinclude methyl, ethyl, n-propyl, iso-propyl, n-butyl, tert-butyl,iso-butyl, sec-butyl, n-pentyl, n-hexyl, n-heptyl, n-octyl, and higherhomologs and isomers.

The term “alkoxy” refers to an alkyl groups attached to the remainder ofthe molecule via an oxygen atom (“oxy”).

The term “cycloalkyl” refers to a saturated or partially unsaturated(non-aromatic) all carbon ring having 3 to 8 carbon atoms (i.e.,(C₃-C₈)carbocycle). The term also includes multiple condensed, saturatedall carbon ring systems (e.g., ring systems comprising 2, 3 or 4carbocyclic rings). Accordingly, carbocycle includes multicycliccarbocyles such as a bicyclic carbocycles (e.g., bicyclic carbocycleshaving about 3 to 15 carbon atoms, about 6 to 15 carbon atoms, or 6 to12 carbon atoms such as bicyclo[3.1.0]hexane and bicyclo[2.1.1]hexane),and polycyclic carbocycles (e.g tricyclic and tetracyclic carbocycleswith up to about 20 carbon atoms). The rings of the multiple condensedring system can be connected to each other via fused, spiro and bridgedbonds when allowed by valency requirements. For example, multicycliccarbocyles can be connected to each other via a single carbon atom toform a spiro connection (e.g., spiropentane, spiro[4,5]decane, etc), viatwo adjacent carbon atoms to form a fused connection (e.g., carbocyclessuch as decahydronaphthalene, norsabinane, norcarane) or via twonon-adjacent carbon atoms to form a bridged connection (e.g.,norbornane, bicyclo[2.2.2]octane, etc). Non-limiting examples ofcycloalkyls include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl,bicyclo[2.2.1]heptane, pinane, and adamantane.

The term “aryl” as used herein refers to a single all carbon aromaticring or a multiple condensed all carbon ring system wherein at least oneof the rings is aromatic. For example, in certain embodiments, an arylgroup has 6 to 20 carbon atoms, 6 to 14 carbon atoms, 6 to 12 carbonatoms, or 6 to 10 carbon atoms. Aryl includes a phenyl radical. Arylalso includes multiple condensed carbon ring systems (e.g., ring systemscomprising 2, 3 or 4 rings) having about 9 to 20 carbon atoms in whichat least one ring is aromatic and wherein the other rings may bearomatic or not aromatic (i.e., cycloalkyl. The rings of the multiplecondensed ring system can be connected to each other via fused, spiroand bridged bonds when allowed by valency requirements. It is to beunderstood that the point of attachment of a multiple condensed ringsystem, as defined above, can be at any position of the ring systemincluding an aromatic or a carbocycle portion of the ring. Non-limitingexamples of aryl groups include, but are not limited to, phenyl,indenyl, indanyl, naphthyl, 1, 2, 3, 4-tetrahydronaphthyl, anthracenyl,and the like.

The term “alkoxycarbonyl” as used herein refers to a group(alkyl)-O—C(═O)—, wherein the term alkyl has the meaning defined herein.

The term “alkanoyloxy” as used herein refers to a group(alkyl)-C(═O)—O—, wherein the term alkyl has the meaning defined herein.

As used herein a wavy line “

” that intersects a bond in a chemical structure indicates the point ofattachment of the bond that the wavy bond intersects in the chemicalstructure to the remainder of a molecule.

The terms “treat”, “treatment”, or “treating” to the extent it relatesto a disease or condition includes inhibiting the disease or condition,eliminating the disease or condition, and/or relieving one or moresymptoms of the disease or condition. The terms “treat”, “treatment” or“treating” also refer to both therapeutic treatment and/or prophylactictreatment or preventative measures, wherein the object is to prevent orslow down (lessen) an undesired physiological change or disorder, suchas, for example, the development or spread of cancer. For example,beneficial or desired clinical results include, but are not limited to,alleviation of symptoms, diminishment of extent of disease or disorder,stabilized (i.e., not worsening) state of disease or disorder, delay orslowing of disease progression, amelioration or palliation of thedisease state or disorder, and remission (whether partial or total),whether detectable or undetectable. “Treat”, “treatment”, or “treating,”can also mean prolonging survival as compared to expected survival ifnot receiving treatment. Those in need of treatment include thosealready with the disease or disorder as well as those prone to have thedisease or disorder or those in which the disease or disorder is to beprevented. In one embodiment “treat”, “treatment”, or “treating” doesnot include preventing or prevention,

The phrase “therapeutically effective amount” or “effective amount”includes but is not limited to an amount of a compound of the that (i)treats or prevents the particular disease, condition, or disorder, (ii)attenuates, ameliorates, or eliminates one or more symptoms of theparticular disease, condition, or disorder, or (iii) prevents or delaysthe onset of one or more symptoms of the particular disease, condition,or disorder described herein.

The term “mammal” as used herein refers to humans, higher non-humanprimates, rodents, domestic, cows, horses, pigs, sheep, dogs and cats.In one embodiment, the mammal is a human. The term “patient” as usedherein refers to any animal including mammals. In one embodiment, thepatient is a mammalian patient. In one embodiment, the patient is ahuman patient.

The compounds disclosed herein can also exist as tautomeric isomers incertain cases. Although only one delocalized resonance structure may bedepicted, all such forms are contemplated within the scope of theinvention.

It is understood by one skilled in the art that this invention alsoincludes any compound claimed that may be enriched at any or all atomsabove naturally occurring isotopic ratios with one or more isotopes suchas, but not limited to, deuterium (²H or D). As a non-limiting example,a —CH₃ group may be substituted with —CD₃. When a compound is shown ornamed as containing a specific isotope, it is understood that thecompound is enriched in that isotope above the natural abundance of thatisotope. In one embodiment the compound may be enriched by at least2-times the natural abundance of that isotope. In one embodiment thecompound may be enriched by at least 10-times the natural abundance ofthat isotope. In one embodiment the compound may be enriched by at least100-times the natural abundance of that isotope. In one embodiment thecompound may be enriched by at least 1000-times the natural abundance ofthat isotope.

The pharmaceutical compositions of the invention can comprise one ormore excipients. When used in combination with the pharmaceuticalcompositions of the invention the term “excipients” refers generally toan additional ingredient that is combined with the compound of formula(I) or the pharmaceutically acceptable salt thereof to provide acorresponding composition. For example, when used in combination withthe pharmaceutical compositions of the invention the term “excipients”includes, but is not limited to: carriers, binders, disintegratingagents, lubricants, sweetening agents, flavoring agents, coatings,preservatives, and dyes.

Stereochemical definitions and conventions used herein generally followS. P. Parker, Ed., McGraw-Hill Dictionary of Chemical Terms (1984)McGraw-Hill Book Company, New York; and Eliel, E. and Wilen, S.,“Stereochemistry of Organic Compounds”, John Wiley & Sons, Inc., NewYork, 1994. The compounds of the invention can contain asymmetric orchiral centers, and therefore exist in different stereoisomeric forms.It is intended that all stereoisomeric forms of the compounds of theinvention, including but not limited to, diastereomers, enantiomers andatropisomers, as well as mixtures thereof such as racemic mixtures, formpart of the present invention. Many organic compounds exist in opticallyactive forms, i.e., they have the ability to rotate the plane ofplane-polarized light. In describing an optically active compound, theprefixes D and L, or R and S, are used to denote the absoluteconfiguration of the molecule about its chiral center(s). The prefixes dand l or (+) and (−) are employed to designate the sign of rotation ofplane-polarized light by the compound, with (−) or l meaning that thecompound is levorotatory. A compound prefixed with (+) or d isdextrorotatory. For a given chemical structure, these stereoisomers areidentical except that they are mirror images of one another. A specificstereoisomer can also be referred to as an enantiomer, and a mixture ofsuch isomers is often called an enantiomeric mixture. A 50:50 mixture ofenantiomers is referred to as a racemic mixture or a racemate, which canoccur where there has been no stereoselection or stereospecificity in achemical reaction or process. The terms “racemic mixture” and “racemate”refer to an equimolar mixture of two enantiomeric species, devoid ofoptical activity. It is to be understood that the present inventionencompasses any racemic, optically-active, polymorphic, orstereoisomeric form, or mixtures thereof, of a compound of theinvention, which possess the useful properties described herein, itbeing well known in the art how to prepare optically active forms (forexample, by resolution of the racemic form by recrystallizationtechniques, by synthesis from optically-active starting materials, bychiral synthesis, or by chromatographic separation using a chiralstationary phase.

When a bond in a compound formula herein is drawn in anon-stereochemical manner (e.g, flat), the atom to which the bond isattached includes all stereochemical possibilities. When a bond in acompound formula herein is drawn in a defined stereochemical manner(e.g. bold, bold-wedge, dashed or dashed-wedge), it is to be understoodthat the atom to which the stereochemical bond is attached is enrichedin the absolute stereoisomer depicted unless otherwise noted. In oneembodiment, the compound may be at least 51% the absolute stereoisomerdepicted. In another embodiment, the compound may be at least 60% theabsolute stereoisomer depicted. In another embodiment, the compound maybe at least 80% the absolute stereoisomer depicted. In anotherembodiment, the compound may be at least 90% the absolute stereoisomerdepicted. In another embodiment, the compound may be at least 95% theabsolute stereoisomer depicted. In another embodiment, the compound maybe at least 99% the absolute stereoisomer depicted.

The term “residue” as it applies to the residue of a compound refers toa compound that has been modified in any manner which results in thecreation of an open valence wherein the site of the open valence. Theopen valence can be created by the removal of 1 or more atoms from thecompound (e.g., removal of a single atom such as hydrogen or removal ofmore than one atom such as a group of atoms including but not limited toan amine, hydroxyl, methyl, amide (e.g., —C(═O)NH₂) or acetyl group).The open valence can also be created by the chemical conversion of afirst function group of the compound to a second functional group of thecompound (e.g., reduction of a carbonyl group, replacement of a carbonylgroup with an amine,) followed by the removal of 1 or more atoms fromthe second functional group to create the open valence.

Specific values listed below for radicals, substituents, and ranges, arefor illustration only; they do not exclude other defined values or othervalues within defined ranges for the radicals and substituents. It is tobe understood that two or more values may be combined. It is also to beunderstood that the values listed herein below (or subsets thereof) canbe excluded.

Specifically, (C₁-C₈)alkyl can be methyl, ethyl, propyl, isopropyl,butyl, iso-butyl, sec-butyl, pentyl, 3-pentyl, or hexyl;(C₁-C₄)cycloalkyl can be cyclopropyl, cyclobutyl, cyclopentyl, orcyclohexyl; (C₁-C₈)alkoxy can be methoxy, ethoxy, propoxy, isopropoxy,butoxy, iso-butoxy, sec-butoxy, pentoxy, 3-pentoxy, or hexyloxy;(C₁-C₈)alkanoyl can be acetyl, propanoyl or butanoyl;(C₁-C₈)alkoxycarbonyl can be methoxycarbonyl, ethoxycarbonyl,propoxycarbonyl, isopropoxycarbonyl, butoxycarbonyl, pentoxycarbonyl, orhexyloxycarbonyl; (C₂-C₈)alkanoyloxy can be acetoxy, propanoyloxy,butanoyloxy, isobutanoyloxy, pentanoyloxy, or hexanoyloxy; and aryl canbe phenyl, indenyl, or naphthyl.

In one embodiment R¹ is H.

In one embodiment R¹ is (C₁-C₄)alkyl.

In one embodiment R¹ is H, methyl, or CD₃.

In one embodiment R² is H.

In one embodiment R² is (C₁-C₄)alkyl.

In one embodiment R² is H or methyl.

In one embodiment R² is H and R⁴ is —N(R^(a))SO₂R^(c).

In one embodiment R³ is —N(R^(a))SO₂R^(c) and R⁴ is H.

In one embodiment R³ is H and R⁴ is —N(R^(a))C(═S)N(R^(a))R^(c).

In one embodiment R³ is —N(R^(a))C(═S)N(R^(a))R^(c) and R⁴ is H.

In one embodiment each R^(a) is H.

In one embodiment each R^(a) is (C₁-C₄)alkyl.

In one embodiment each R^(a) is methyl.

In one embodiment R^(c) is (C₂-C₆)alkyl that is optionally substitutedwith one or more groups independently selected from the group consistingof halo and cyano.

In one embodiment R^(c) is (C₃-C₆)alkyl that is optionally substitutedwith one or more groups independently selected from the group consistingof halo and cyano.

In one embodiment R_(c) is (C₃-C₅)alkyl that is optionally substitutedwith one or more groups independently selected from the group consistingof halo and cyano.

In one embodiment R^(c) is (C₃-C₄)alkyl that is optionally substitutedwith one or more groups independently selected from the group consistingof halo and cyano.

In one embodiment R^(c) is butyl, 4-cyanobutyl, or cyclohexyl.

One embodiment provides a compound of formula (Ia):

or a salt thereof.

One embodiment provides a compound of formula (Ib):

or a salt thereof.

One embodiment provides a compound of formula (Ic):

or a salt thereof.

One embodiment provides a compound of formula (Id):

or a salt thereof.

One embodiment provides a compound of formula (Ie):

wherein R² is H, halo, or (C₁-C₄)alkyl or a salt thereof.

In one embodiment R¹ is H.

In one embodiment R¹ is methyl or CD3.

In one embodiment R² is H.

One embodiment provides a compound selected from the group consistingof:

or a salt thereof.

In one embodiment, R¹ is H, or (C₁-C₄)alkyl; R² is H, (C₁-C₄)alkyl, orhalo; R³ is H and R⁴ is —N(R^(a))SO₂R^(c) or—N(R^(a))C(═S)N(R^(a))R^(c); or R³ is —N(R^(a))SO₂R^(c) or—N(R^(a))C(═S)N(R^(a))R^(c) and R⁴ is H; and each R^(a) is independentlyH or (C₁-C₄)alkyl; and R^(c) is (C₃-C₆)cycloalkyl, or (C₂-C₆)alkyl,wherein any (C₃-C₆)cycloalkyl and (C₂-C₆)alkyl is optionally substitutedwith one or more groups independently selected from the group consistingof halo, and cyano.

In cases where compounds are sufficiently basic or acidic, a salt of acompound of formula I can be useful as an intermediate for isolating orpurifying a compound of formula I. Additionally, administration of acompound of formula I as a pharmaceutically acceptable acid or base saltmay be appropriate. Examples of pharmaceutically acceptable salts areorganic acid addition salts formed with acids which form a physiologicalacceptable anion, for example, tosylate, methanesulfonate, acetate,citrate, malonate, tartarate, succinate, benzoate, ascorbate,α-ketoglutarate, and α-glycerophosphate. Suitable inorganic salts mayalso be formed, including hydrochloride, sulfate, nitrate, bicarbonate,and carbonate salts.

Salts may be obtained using standard procedures well known in the art,for example by reacting a sufficiently basic compound such as an aminewith a suitable acid affording a physiologically acceptable anion.Alkali metal (for example, sodium, potassium or lithium) or alkalineearth metal (for example calcium) salts of carboxylic acids can also bemade.

The compounds of formula I can be formulated as pharmaceuticalcompositions and administered to a mammalian host, such as a humanpatient in a variety of forms adapted to the chosen route ofadministration, i.e., orally or parenterally, by intravenous,intramuscular, topical or subcutaneous routes.

Thus, the present compounds may be systemically administered, e.g.,orally, in combination with a pharmaceutically acceptable vehicle suchas an inert diluent or an assimilable edible carrier. They may beenclosed in hard or soft shell gelatin capsules, may be compressed intotablets, or may be incorporated directly with the food of the patient'sdiet. For oral therapeutic administration, the active compound may becombined with one or more excipients and used in the form of ingestibletablets, buccal tablets, troches, capsules, elixirs, suspensions,syrups, wafers, and the like. Such compositions and preparations shouldcontain at least 0.1% of active compound. The percentage of thecompositions and preparations may, of course, be varied and mayconveniently be between about 2 to about 60% of the weight of a givenunit dosage form. The amount of active compound in such therapeuticallyuseful compositions is such that an effective dosage level will beobtained. The tablets, troches, pills, capsules, and the like may alsocontain the following: binders such as gum tragacanth, acacia, cornstarch or gelatin; excipients such as dicalcium phosphate; adisintegrating agent such as corn starch, potato starch, alginic acidand the like; a lubricant such as magnesium stearate; and a sweeteningagent such as sucrose, fructose, lactose or aspartame or a flavoringagent such as peppermint, oil of wintergreen, or cherry flavoring may beadded. When the unit dosage form is a capsule, it may contain, inaddition to materials of the above type, a liquid carrier, such as avegetable oil or a polyethylene glycol. Various other materials may bepresent as coatings or to otherwise modify the physical form of thesolid unit dosage form. For instance, tablets, pills, or capsules may becoated with gelatin, wax, shellac or sugar and the like. A syrup orelixir may contain the active compound, sucrose or fructose as asweetening agent, methyl and propylparabens as preservatives, a dye andflavoring such as cherry or orange flavor. Of course, any material usedin preparing any unit dosage form should be pharmaceutically acceptableand substantially non-toxic in the amounts employed. In addition, theactive compound may be incorporated into sustained-release preparationsand devices.

The active compound may also be administered intravenously orintraperitoneally by infusion or injection. Solutions of the activecompound or its salts can be prepared in water, optionally mixed with anontoxic surfactant. Dispersions can also be prepared in glycerol,liquid polyethylene glycols, triacetin, and mixtures thereof and inoils. Under ordinary conditions of storage and use, these preparationscontain a preservative to prevent the growth of microorganisms.

The pharmaceutical dosage forms suitable for injection or infusion caninclude sterile aqueous solutions or dispersions or sterile powderscomprising the active ingredient which are adapted for theextemporaneous preparation of sterile injectable or infusible solutionsor dispersions, optionally encapsulated in liposomes. In all cases, theultimate dosage form should be sterile, fluid and stable under theconditions of manufacture and storage. The liquid carrier or vehicle canbe a solvent or liquid dispersion medium comprising, for example, water,ethanol, a polyol (for example, glycerol, propylene glycol, liquidpolyethylene glycols, and the like), vegetable oils, nontoxic glycerylesters, and suitable mixtures thereof. The proper fluidity can bemaintained, for example, by the formation of liposomes, by themaintenance of the required particle size in the case of dispersions orby the use of surfactants. The prevention of the action ofmicroorganisms can be brought about by various antibacterial andantifungal agents, for example, parabens, chlorobutanol, phenol, sorbicacid, thimerosal, and the like. In many cases, it will be preferable toinclude isotonic agents, for example, sugars, buffers or sodiumchloride. Prolonged absorption of the injectable compositions can bebrought about by the use in the compositions of agents delayingabsorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions are prepared by incorporating the activecompound in the required amount in the appropriate solvent with variousof the other ingredients enumerated above, as required, followed byfilter sterilization. In the case of sterile powders for the preparationof sterile injectable solutions, the preferred methods of preparationare vacuum drying and the freeze drying techniques, which yield a powderof the active ingredient plus any additional desired ingredient presentin the previously sterile-filtered solutions. For topicaladministration, the present compounds may be applied in pure form, i.e.,when they are liquids. However, it will generally be desirable toadminister them to the skin as compositions or formulations, incombination with a dermatologically acceptable carrier, which may be asolid or a liquid.

Useful solid carriers include finely divided solids such as talc, clay,microcrystalline cellulose, silica, alumina and the like. Useful liquidcarriers include water, alcohols or glycols or water-alcohol/glycolblends, in which the present compounds can be dissolved or dispersed ateffective levels, optionally with the aid of non-toxic surfactants.Adjuvants such as fragrances and additional antimicrobial agents can beadded to optimize the properties for a given use. The resultant liquidcompositions can be applied from absorbent pads, used to impregnatebandages and other dressings, or sprayed onto the affected area usingpump-type or aerosol sprayers.

Thickeners such as synthetic polymers, fatty acids, fatty acid salts andesters, fatty alcohols, modified celluloses or modified mineralmaterials can also be employed with liquid carriers to form spreadablepastes, gels, ointments, soaps, and the like, for application directlyto the skin of the user.

Examples of useful dermatological compositions which can be used todeliver the compounds of formula i to the skin are known to the art; forexample, see Jacquet et al. (U.S. Pat. No. 4,608,392), Geria (U.S. Pat.No. 4,992,478), Smith et al. (U.S. Pat. No. 4,559,157) and Wortzman(U.S. Pat. No. 4,820,508).

Useful dosages of the compounds of formula I can be determined bycomparing their in vitro activity, and in vivo activity in animalmodels. Methods for the extrapolation of effective dosages in mice, andother animals, to humans are known to the art; for example, see U.S.Pat. No. 4,938,949.

The amount of the compound, or an active salt or derivative thereof,required for use in treatment will vary not only with the particularsalt selected but also with the route of administration, the nature ofthe condition being treated and the age and condition of the patient andwill be ultimately at the discretion of the attendant physician orclinician.

The desired dose may conveniently be presented in a single dose or asdivided doses administered at appropriate intervals, for example, astwo, three, four or more sub-doses per day. The sub-dose itself may befurther divided, e.g., into a number of discrete loosely spacedadministrations; such as multiple inhalations from an insufflator or byapplication of a plurality of drops into the eye.

Compounds of the invention can also be administered in combination withother therapeutic agents, for example, other antibacterial agents.Examples of such agents include isoniazid. Accordingly, in oneembodiment the invention also provides a composition comprising acompound of formula I, or a pharmaceutically acceptable salt thereof, atleast one other therapeutic agent, and a pharmaceutically acceptableexcipient. The invention also provides a kit comprising a compound offormula I, or a pharmaceutically acceptable salt thereof, at least oneother therapeutic agent, packaging material, and instructions foradministering the compound of formula I or the pharmaceuticallyacceptable salt thereof and the other therapeutic agent or agents to ananimal to treat a bacterial infection. The invention will now beillustrated by the following non-limiting Examples.

EXAMPLES Example 1

Bacterial Strains, Culture Conditions, Primers and Plasmids.

M. tuberculosis strains were obtained from laboratory stocks. Clinicalstrains were obtained from a collection of clinical isolates forResearch and Training in Tropical Diseases (TDR) established byUNICEF/UNDP/World Bank/WHO Special Programs. All M. tuberculosis strainswere grown at 37° C. in Middlebrook medium 7H9 (Becton Dickinson,Sparks, Md.) enriched with 10% oleic acid-albumin-dextrose-catalase(OADC-Becton Dickinson) or 1×ADS (albumin (0.5 g/L)-dextrose (0.2g/L)-sodium chloride (0.081 g/L)) and Tween 80 0.05% (wt/v) or tyloxapol(0.05% (wt/v) in liquid media. Middlebrook 7H10 agar (Becton Dickinson)supplemented with 10% OADC and 0.5% glycerol (v/v) was used to growstrains on solid media.

Reporter Screen for Cell-Wall Biosynthesis Inhibitors.

A total of 168 compounds previously identified as having anti-tubercularactivity in a whole-cell screen by GlaxoSmithKline (Ballell, L., et al.,Chem Med Chem, 2013, 8, 313-321) were tested for their ability to inducethe iniBAC promoter (piniBA). The promoter screen used a BCG strain(BCG^(S)(pG4697-6)) harboring the iniBAC promoter sequence fused to alacZ reporter on an integrative plasmid (pG4697-6)(Alland, D., J.Bacteriol, 2000, 182, 1802-1811). The BCG^(S)(pG4697-6) was grown to anOD600 of 0.2-0.3 and 90 μL was dispensed into each well of 96-deep wellplates and then 10 μL of each compound (final concentration 10 μM) wasadded and incubated at 37° C. under shaking at 250 rpm. After incubationfor 24 h, 100 μL of Lac Z buffer (60 mM Na₂HPO₄.7H₂O, 40 mM NaH₂PO₄.H₂O,10 mM KCl, 1 mM MgSO₄.7H₂O, 50 mM β-mercaptoethanol) was added followedby addition of 5 μL of chloroform and 2 μL of 0.1% SDS and incubated for5 minutes at room temperature (RT). Then, 40 μL of 4 mg/mL of LacZsubstrate (2-nitrophenyl β-D-galactopyranoside, Sigma-Aldrich, St.Louis, Mo.) was added to each well and plates were incubated for 15 min.The reactions were terminated by adding 100 μL of 1 M aqueous sodiumcarbonate and absorbance was read at 420 nm. Fold induction wasdetermined by OD₄₂₀ with compounds/OD₄₂₀ of vehicle (DMSO) controls. EMBand INH were used as positive controls.

Minimal Inhibitory Concentration (MIC) and Drug Interaction.

MIC assays in 96-well format were performed using the microdilutionmethod (Kim, P., et al., J. Ma. Chem., 2009, 52, 1329-1344). MICs wereperformed in 96 well plates using microdilution alamar blue (MABA)method. Briefly, the drugs were serially diluted in 50 μL of growthmedia (7H9-ADS) and supplemented 50 μL diluted cultures (1:1000) of M.tuberculosis grown to OD₅₉₅=0.2-0.3. After incubation for 7 days at 37°C., AlamarBlue® Cell Viability Reagent (ThermoFischer Scientific, GrandIsland, N.Y., USA) was added, the cultures were incubated for another 24hours, and then the absorbance was read at 570 nm and normalized to 6010nM as per manufacturer's instruction. A checkerboard analysis (Reddy, V.M., et al., Antimicrobial Agents and Chemotherapy, 2010, 54, 2840-2846)was used to determine synergy and antagonism of the DG167 with INH. Thefractional inhibitory concentration (FIC) was determined by dividing theMIC of the combination of drugs by the MIC of the drugs independently.Fractional inhibitory index (ΣFIC) was determined by adding the FICs ofeach drug tested. Activity of compounds were defined as synergistic ifΣFIC≤0,5, antagonistic if ΣFIC≥4.0, and additive if ΣFIC>0.5 and <4.0(Reddy et al., 2010).

Isolation of Resistant Mutants and Whole-Genome Sequencing.

The DG167-resistant Mtb mutants were isolated by plating 106-108 M.tuberculosis cells onto 71410 plates containing 1×-32× of DG167. Plateswere screened for DG167 resistant colonies after 3-4 weeks at 37° C. Thegenomic DNA was isolated (van Soolingen, D., et al., Journal of ClinicalMicrobiology, 1991, 29, 2578-2586) and subjected to whole-genomesequencing and single nucleotide polymorphism (SNP) analysis (Tahlan,K., et al., Antimicrob Agents Chemother, 2012, 56, 1797-1809).

Cloning and Purification of His-KasA.

M. tuberculosis kasA gene was PCR amplified using AccuPrime™ SuperMix(ThermoFischer Scientific) and primers (kasA-NheI: 5′CGAGGCTTGAGGCCGAGCTA-GCGTGAGTCAGCCTTC 3′ and kasA-HindIII: 5′CCCGCGATGTCAAGCTTCAGTAACG 3′). The kasA amplicon was cloned between NheIHindIII restriction sites in pET28b plasmid inserting N-terminus his %tag. The kasA along with his tag was again PCR amplified usingAccuPrime™ SuperMix and primers (kasA-SR113-Inf-Fp: 5′AAAGGGAGTCCATATGGGCAGCAGCCATCATCAT 3′ and kasA-SR113-Inf-Fp: 5′GATAAGCTTCGAATTCTCAGTAACGCCCGAAGGC 3′) and cloned in an acetamideinducible mycobacterial expression vector, pSR113 (Ryndak, M. B., etal., J Bacteriol, 2010, 192, 861-869) between NdeI-EcoRI usingIn-Fusion® HD Cloning kit (Takara Bio USA). The resultant constructpSR113-hisN-kasA was transformed into Mycobacterium smegmatis mc²155.His-KasA was overexpressed in M. smegmatis grown in LB mediumsupplemented with 30 μg/mL kanamycin and 0.02% Tween-80 to an OD₆₀₀ of0.6 at 37° C. Expression was induced with 0.02% w/v acetamide for 36hours at 37° C. KasA was then purified using a modified version of apreviously described protocol (Luckner, S. R., et al., Structure, 2009,17, 1004-1013). Briefly, following expression the bacterial cells werecollected via centrifugation at 5,000×g for 30 minutes and stored at−80° C. The cell pellet was resuspended in Buffer A [500 mM NaCl and 20mM CHES (pH 9.5)] accompanied by 20 μg/mL DNase. Cells were then lysedvia French Press at 15,000 psi and insoluble cell debris was separatedvia centrifugation at 25,000×g for 45 minutes. Lysate supernatant wasapplied to His-60 Ni Resin (Clontech) equilibrated in Buffer A, and KasAwas eluted with Buffer A containing 200 mM imidazole. The eluted proteinwas then diluted to a final NaCl concentration of 50 mM using 20 mM CHES(pH 9.5) and loaded onto a MonoQ anion exchange column (GE Healthcare)equilibrated in 20 mM CHES (pH 9.5). KasA was eluted in a 50-1000 mMNaCl gradient of 20 mM CHES (pH 9.5) over 20 CV. Fractions containingKasA were pooled, concentrated using 10,000 molecular weight cutoffcentrifugal filter units at 4,000×g, and further purified by passageover a Superdex-S200 16/70 (GE Healthcare) equilibrated in Buffer A. Thefinal protein was then filtered through 0.22 μM Costar spin filters andstored at 4° C. All protein concentrations were determined by UVspectroscopy at 280 nm using molar extinction coefficientsexperimentally derived by the method of Gill and von Hippel (Gill, S.C., and von Hippel, P. H., Anal Biochem, 1989, 182, 319-326).

Crystallization and Data Collection.

KasA crystals were produced by the vapor diffusion method at 20° C. with4.7 mg/mL of KasA in 2 μL hanging drops mixed 1:1 with mother liquorcontaining 200 mM NaCl with either 8% isopropanol and 1 mMTris(2-carboxyethyl)phosphine hydrochloride (TCEP HCl) or 14%isopropanol and 2 mM TCEP HCl. Crystals from the condition containing 8%isopropanol were used to determine the structure of KasA-DG167 andExample 29 (trideuteriomethyl analog of DG167), while crystals from thecondition containing 14% isopropanol were used to determine thestructure of apo KasA. These conditions are similar but not identical tothose previously used for crystallographic studies of KasA, whichcontained 10% isopropanol, 200 mM NaCl, 100 mM HEPES (7.5), and 10 mMTCEP HCl (Luckner, S. R., et al., Structure, 2009, 17, 1004-1013).KasA-DG167 crystals were obtained by moving apo KasA crystals from thehanging drops to 5 μL of soaking solutions containing 1 mM DG167, 8%isopropanol, 1 mM TCEP, 200 mM NaCl, and 1% DMSO for 1 h. After 1 hour,the soaked crystal was placed in the same solution supplemented with 30%glycerol, immediately removed from the drop, and then flash-cooled inliquid nitrogen. Example 29 crystals were obtained in an identicalmanner by substituting the DG167 for 1 mM. Example 29. KasA-Example 41crystals were grown in a similar manner with the following modification:the 2 μL hanging drops contained 1 μL of mother liquor and 1 μL ofpurified 110 μM KasA and 1 mM Example 41. The KasA-Example 41 crystalsselected for data collection grew over the course of seven days in 200mM NaCl, 2 mM TCEP HCl, and 4% isopropanol. These crystals werecryo-protected in their crystallization condition supplemented with 22%glycerol and 1 mM Example 41.

X-ray diffraction data were collected using single crystals mounted innylon loops that were then flash-cooled in liquid nitrogen before datacollection in a stream of dry N₂ at 100 K. ata sets for apo KasA,KasA-DG167, and Example 29 were collected at the Stanford SynchrotronRadiation Lightsource (SSRL) beamline 14-1 at 1.1808 Å with a MARmosaic325 CCD detector. The KasA-5g data set was collected on beamline 9-2 at0.88557 Å with a Dectris Pilatus 6M detector. X-ray data were processedusing HKL2000 (Otwinowski, Z., and Minor, W. Methods Enzymol, 1997, 276,307-326). Crystallographic phases for apo KasA were determined bymolecular replacement using Phaser (McCoy, A. J., et al., J ApplCrystallogr, 2007, 40, 658-674) and the previously determined structureof apo KasA (PDB Code: 2WGD) as a search model (Luckner, S. R., et al.,Structure, 2009, 17, 1004-1013). Crystallographic phases for KasA-DG167,Example 29, and KasA-Example 41 were determined by molecular replacementusing Phaser (McCoy, A. J., et al., J Appl Crystallogr, 2007, 40,658-674) and the previously determined structure of KasA bound to TLM5(PDB Code: 4C6U) (Schiebel, J., et al., J Biol Chem, 2013, 288,34190-34204). Models were generated using iterative cycles of modelbuilding in Coot (Emsley, P., et al., Acta Cryslallogr D BiolCrysallogr, 2010, 66, 486-501) and refinement in phenix.refine (Adams etal., 2010). Initial refinement included simulated annealing as well asrigid body, individual atomic coordinate, and individual B-factorrefinement. Later rounds of refinement employed individual atomiccoordinate, individual B-factor, and TLS refinement. TLS groups wereselected using the TLSMD server (Painter and Merritt, 2006). During thefinal rounds of refinement, the stereochemistry and ADP weights wereoptimized. DG167, Example 29, and water molecules were included onlyafter the KasA models were complete. Insufficient electron density wasobserved for the following residues in flexible regions of thestructures, and they were omitted from the model: apo KasA 1-25;KasA-DG167 1-25; Example 29 1-25. One sodium atom was built into clearelectron density during the final stages of refinement. Ramachandranstatistics were calculated in Molprobity (Lovell et al., 2003).Molecular graphics were produced with PyMOL (Delano, W. L. The PyMOLMolecular Graphics System, 2002).

Microscale Thermophoresis Binding Assays.

Prior to labeling. His-KasA was diluted from 100 μM in Buffer A to 200nM in Buffer B (10 mM HEPES, 150 mM NaCl, pH 7.4). The diluted His-KasAwas labeled using the RED-tris-NTA His-Tag Labeling kit (NanoTemperTechnologies). 50 nM working stocks of labeled protein were madeconsisting of Buffer B supplemented with 0.1% Pluronic F-127. Threefoldtitrations of Example 1 and DG167 in DMSO were made, transferred byLabcyte 555 ECHO instrument into separate 384-well polypropylene plates,and incubated with 50 nM working stock solutions of labeled protein inthe dark for 30 min at room temperature. After incubation, the sampleswere transferred into Premium Coated Capillaries and read in a MonolithNT.115 Nano-BLUE/RED Instrument at room temperature using 60% LED and60% MST power for DG167, and 60% LED and 40% MST power for Example 1.Binding affinities were calculated using the Thermophoresis with T JumpEvaluation strategy from a minimum of three experiments.

Analysis of Mycolic Acids.

The MAMEs and FAMEs (Slayden, R. A., and Barry. C. E., 3^(rd) ,Molecular Medicine, 2001, 54, 229-245) were analyzed as describedpreviously. The compounds were added to 5 mL of M. tuberculosis cultures(OD595 of ˜0.3-0.4), incubated at 37° C. for 2 hours and 1 μCi/mL of14C-acetate (56 mCi/mmol) was added to each culture, followed byincubation at 37° C. for another 4 hours. The 14C-labeled cells werepelleted by centrifugation, resuspended in 2 mL of tetra-n-butylammoniumhydroxide (TBAH) and incubated overnight at 100° C. to hydrolyzecell-wall bound lipids. The fatty acids were esterified by adding 4 mLCH2Cl2, 300 μL iodomethane, and 2 mL distilled water (dH2O) and mixingat room temperature for 1 hour, the phases were separated bycentrifugation, the upper aqueous phase was discarded and the lowerorganic phase was washed twice with dH2O, dried and resuspended in 3 mLof diethyl ether. Insoluble material was removed by centrifugation, theorganic phase was dried and lipids were resuspended in 200 μL CH₂Cl₂.Equal counts (20,000 cpm) were loaded on a silica gel 60 F254 thin-layerchromatography (TLC) plate and resolved using hexane/ethyl acetate(19:1, v/v, 2 runs). The FAMEs and MAMEs were detected byphosphorimaging.

Killing Studies Using CFU Measurements.

M. tuberculosis cells (˜107 CFU/mL) were treated with compounds,incubated at 37° C. under shaking, the samples were drawn at specifictime points and total viable counts determined by dilution plating on7H10-OADC-agar plates and counting colony forming units after 4-weekincubation at 37° C.

RNAseq Analysis.

M. tuberculosis H37Rv was grown to OD595 to ˜0.4 tissue culture flasks(50 mL each) and pooled. The cultures (10 mL) were redistributed intoflasks containing each compound or compound combination or vehicle(DMSO) control. The final concentration of DMSO was kept constant ineach flask. After 4 h incubation at 37° C. with shaking, the cultureswere harvested by centrifugation and total RNA was extracted usingTRIzol® LS reagent (ThermoFisher Scientific) and bead beating followedby extraction with the RNeasy® Mini Kit (Qiagen) as described (Malherbeet al., 2016). The integrity and purity of RNA was determined bybioanalyzer (2100, Agilent), rRNA was removed, and the cDNA library wasprepared. The sequencing of the cDNA libraries was performed on theIllumina NextSeq 500 platform (Illumina, San Diego, Calif.) using thehigh output 1×75 cycles configuration. CLC Genomics Workbench 9.0.1version (http://www.clcbio.com/products/clc-genomics-workbench/; Qiagen)was utilized for RNA-seq analysis. De-multiplexed fastq files fromRNA-Seq libraries were imported into the CLC software. Bases with lowquality were trimmed and reads were mapped to the reference genome,Mycobacterium tuberculosis H37Rv (NCBI Reference Sequence: NC_000962_3).The aligned reads were obtained using the RNA-Seq Analysis Tool of CLCGenomics Workbench. RPKM values were calculated for each gene toquantify absolute expression. Statistical analysis of differentiallyexpressed genes was carried out with the Empirical analysis of DigitalGene Expression data tool in CLC Genomic Workbench. Replicates wereaveraged, and genes with FDR adjusted p value <0.05 and fold change ofan absolute value >2.0 were identified.

Mouse Pharmacokinetic Studies.

All animal experiments were conducted in compliance with and approved bythe Institutional Animal Care and Use Committee of the New JerseyMedical School, Rutgers University. Female BALB/c mice were weighed(23-29 g) and treated via oral gavage with a single dose of DG167 (100mg/kg) formulated in 0.5% CMC/0.5% Tween 80. Sequential bleeds werecollected at 0.25, 0.5, 1, 3, 5 and 8 h post-dose via tail snip method.Blood (50 μL) was collected in capillary microvette EDTA blood tubes andkept on ice prior to centrifugation at 1,500 g for 5 minutes. Thesupernatant (plasma) was transferred into a 96-well plate and stored at−80° C. In a dose escalation study, mice were dosed with 50, 100, 250 or50) mg/kg DG167, and blood was similarly sampled and processed.

Quantitative Analysis.

DG1167 levels in plasma were measured by LC-MS/MS in electrospraypositive-ionization mode (ESI+) on a Sciex Qtrap 4000 triple-quadrupolemass combined with an Agilent 1260 HPLC using Analyst software.Chromatography was performed with an Agilent Zorbax SB-C8 column (2.1×30mm, particle size, 3.5 μm) using a reverse phase gradient elution. 0.1%formic acid in Milli-Q deionized water was used for the aqueous mobilephase and 0.1% formic acid in acetonitrile (ACN) for the organic mobilephase. Multiple-reaction monitoring (MRM) of parent/daughter transitionsin electrospray positive-ionization mode (ESI+) was used to quantifyDG167. A DMSO stock of DG167 was serial diluted in blank K2EDTA plasma(Bioreclammation) to create standard curves and quality control samples.DG167 was extracted by combining 20 μL of spiked plasma or study samplesand 200 μL of acetonitrile/methanol (50150) protein precipitationsolvent containing 20 ng/mL verapamil internal standard (IS). Extractswere vortexed for 5 minutes and centrifuged at 4000 RPM for 5 minutes.The supernatants were analyzed by LC-MS. Verapamil IS was sourced fromSigma-Aldrich. The following MRM transitions were used for DG167(268.1/146) and verapamil (455.4/165.2). Sample analysis was accepted ifthe concentrations of the quality control samples were within 20% of thenominal concentration.

Drug Tolerability.

Five mice were dosed orally daily for 5 days with DG167 (100 mg/kg)formulated in 0.5% CMC/0.5% Tween 80 and INH (25 mg/kg) in water. Priorto dosing, DG167 and INH were mixed (1:1) and vortexed. The mice wereweighed and observed daily. Their behavior, drinking and feedingpatterns, and feces were monitored and recorded. Upon necropsy, liver,gall bladder, kidney and spleen pathology were observed as well.

Mouse Efficacy.

Nine week-old female BALB/c mice (weight range 18-20 g) were infectedwith an inoculum of M. tuberculosis H37Rv in 5 mL of PBS (3×106 CFU/mL)using a Glas-Col whole body aerosol unit. This resulted in lungimplantation of 1.09 log 10 CFU per mouse. Groups of 5 mice weresacrificed by cervical dislocation at the start of treatment (2-weekpost-infection), and after receiving DG167 at 100 mg/kg, INH at 25mg/kg, the combination (DG167 at 100 mg/kg+INH at 25 mg/kg) or thevehicle only for 3 days, 1 week, or 2 weeks daily. Whole lungs werehomogenized in 5 mL of PBS containing 0.05% Tween 80. CFU weredetermined by plating serial dilutions of homogenates onto Middlebrook7H11 agar with OADC. Colonies were counted after at least 21 days ofincubation at 37° C.

Synthesis of DG167 and its Analogs.

All reagents were purchased from commercial suppliers and used withoutfurther purification unless noted otherwise. All chemical reactionsoccurring solely in an organic solvent were carried out under an inertatmosphere of argon or nitrogen. Analytical TLC was performed with Mercksilica gel 60 F254 plates. Silica gel column chromatography wasconducted with Teledyne Isco CombiFlash Companion or Rf+ systems. ¹H NMRspectra were acquired on Bruker 500 MHz instruments and are listed inparts per million downfield from TMS. LC-MS was performed on an Agilent1260 HPLC coupled to an Agilent 6120 MS. All synthesized compounds wereat least 95% pure as judged by their HPLC trace at 250 nm and werecharacterized by the expected parent ion(s) in the MS.

Synthesis of 1-methyl-6-nitro-1H-indazole (2a, FIG. 7)

To a vigorously stirring, ice cold solution of 6-nitro-1H-indazole (4.14g, 25.4 mmol) in dimethylformamide (100 mL), NaH (2.03 g, 50.7 mmol) wasadded in four portions. The reaction mixture was maintained at 0° C. for30 minutes. Iodomethane (1.74 mL, 27.9 mmol) was added dropwise to thereaction mixture and the reaction was stirred for 16 hours at roomtemperature. The reaction mixture was quenched with water and dilutedwith ethyl acetate. The reaction mixture was transferred to a separatoryfunnel, washed with water three times and dried over anhydrous magnesiumsulfate. The reaction mixture was concentrated on a rotary evaporatorand 1-methyl-6-nitro-1H-indazole was separated from2-methyl-6-nitro-2H-indazole by flash chromatography on silica usingethyl acetate as eluent to afford the product as a yellow solid (2.54 g,56.4% yield): 1H NMR (600 MHz, DMSO) δ 8.73 (s, 1H), 8.29 (s, 1H), 8.01(d, J=8.79 Hz, 1H), 7.95 (dd, J=1.47, 8.79 Hz, 1H), 4.19 (s, 3H).

Using a procedure similar to that described for Compound 2a,1-ethyl-6-nitro-1H-indazole (2b, FIG. 7), 6-nitro-1-propyl-1H-indazole(2c, FIG. 7), 1-benzyl-6-nitro-1H-indazole (2d, FIG. 7), and1-(methyl-d3)-6-nitro-1H-indazole (2e, FIG. 7) were prepared.

Synthesis of 1-isopropyl-6-nitro-1H-indazole (2f, FIG. 7)

A solution of 6-nitro-1H-indazole (378 mg, 2.32 mmol), isopropyl iodide(277.5 μL, 2.780 mmol), copper (1) iodide (22 mg, 0.12 mmol), potassiumphosphate (985 mg, 4.64 mmol). N,N-dimethylethylenediamine (25.3 μL,0.232 mmol) in dimethylformamide (1.2 mL) was stirred at 110° C. for 72h. After completion of the reaction, the reaction mixture was filteredover Celite and the filtrate was diluted with ethyl acetate, transferredto a separatory funnel, washed with water three times and dried overanhydrous magnesium sulfate. The reaction mixture was concentrated on arotary evaporator and 1-isopropyl-6-nitro-1H-indazole was separated from2-isopropyl-6-nitro-2H-indazole by flash chromatography on silica usingethyl acetate as eluent to afford the product as a yellow solid (199 mg,56.4% yield): 1H NMR (500 MHz, CDCl3) δ 7.97 (s, 1H), 7.67 (d, J=8.54Hz, 1H), 7.43 (s, 1H), 6.86 (dd, J=1.8, 8.5 Hz, 1H), 6.63 (s, 1H), 4.80(td, J=6.6, 13.3 Hz, 1H), 3.03-3.20 (m, 2H), 1.72-1.92 (m, 2H), 1.58 (d,J=6.4 Hz, 6+1 H from H2O), 1.31-1.51 (m, 2H), 0.90 (t, J=7.3 Hz, 3H).

Using a procedure similar to that described for Compound 2f,1-phenyl-6-nitro-1H-indazole (2g, FIG. 7) was prepared.

Synthesis of 1-methyl-1H-indazol-6-amine (4a)

To a solution of 1-methyl-6-nitro-1Hindazole (2a) (2.5 g, 14.2 mmol) inethanol (150 mL) was added ammonium formate (7 g) and 10 wt % Pd/C (1g). The mixture maintained under nitrogen was stirred at roomtemperature for 3 hours. After completion of reaction, the Pd/C catalystand excess ammonium formate were removed via filtration of the crudereaction mixture through a pad of Celite. The filtrate was concentratedon the rotary evaporator to remove ethanol. The crude material waspurified by flash chromatography on silica gel to obtain1-methyl-1H-indazol-6-amine (4a) as a light pink solid (1.61 g, 77%yield): ¹H NMR (500 MHz, CDCl3) δ 7.80 (s, 1H), 7.48 (d, J=8.54 Hz, 1H),6.57 (d, J=8.54 Hz, 1H), 6.53 (s, 1H), 3.94 (s, 3H), 3.88 (br s, 2H).

Using a procedure similar to that described for Compound 4a,1-ethyl-1H-indazol-6-amine (4b), 1-propyl-1H-indazol-6-amine (4c),1-benzyl-1H-indazol-6-amine (4d), 1-(methyl-d3)-1Hindazol-6-amine (4e),1-isoproyl-1H-indazol-6-amine (4f), 1-phenyl-1H-indazol-6-amine (4g) and3-methyl-5-nitro-1H-indazole (4h) were prepared.

Synthesis of N-(1-methyl-1H-indazol-6-yl)butane-1-sulfonamide (DG167(5a-1))

To a solution of 1-methyl-1H-indazol-6-amine (464 mg, 3.15 mmol) inpyridine (20 mL) was added n-butyl sulfonyl chloride (450 μL, 3.47 mmol)and the reaction was stirred at room temperature for 16 hours. Aftercompletion of the reaction, the reaction mixture was diluted with ethylacetate and transferred to a separatory funnel. The organic layer waswashed with saturated aqueous sodium bicarbonate solution, followed bywater, and brine. The organic layer was dried over anhydrous magnesiumsulfate, filtered and concentrated. The crude product was purified byflash chromatography on silica gel (gradient: 30-70% ethylacetate/hexanes) to obtain the product as a white solid (700 mg, 83%yield): ¹H NMR (500 MHz, CDCl3) δ 7.94 (s, 1H), 7.67 (d, J=8.5 Hz, 1H),7.39 (s, 1H), 7.11 (br, s., 1H), 6.91 (dd, J=1.8, 8.5 Hz, 1H), 4.05 (s,3H), 3.17-3.09 (m, 2H), 1.89-1.77 (m, 2H), 1.45-1.35 (m, 2H), 0.88 (t,J=7.5 Hz, 3H).

Using a procedure similar to that described for the synthesis of theDG167(5a-1), the following Example compounds 1-31 were prepared.

Example 1 N-(1H-indazol-6-yl)butane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 8.06 (s, 1H), 7.49 (d, J=8.54 Hz, 1H), 6.70(dd, J=1.83, 8.54 Hz, 1H), 4.07 (br s, 1H), 3.31-3.41 (m, 2H), 1.66 (td,J=7.67, 15.49 Hz, 2H), 1.36 (qd, J=7.44, 14.92 Hz, 2H), 0.86 (t, J=7.32Hz, 3H).

Example 2 N-(1-ethyl-1H-indazol-6-yl)butane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.90-8.00 (m, 1H), 7.67 (d, J=8.5 Hz, 1H),7.41 (s, 1H), 6.87 (d, J=8.5 Hz, 1H), 6.77 (s, 1H), 4.41 (q, J=7.3 Hz,2H), 3.07-3.18 (m, 2H), 1.82 (quin, J=7.7 Hz, 2H), 1.51 (t, J 7.3 Hz,3H), 1.41 (qd, J=7.3, 14.9 Hz, 2H), 0.89 (t, J=7.3 Hz, 3H).

Example 3 N-(1-propyl-1H-indazol-6-yl)butane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.95 (s, 1H), 7.67 (d, J=8.54 Hz, 1H), 7.40(s, 1H), 6.85-6.96 (m, 2H), 4.31 (t, J=7.02 Hz, 2H), 3.06-3.16 (m, 2H),1.89-1.99 (m, 2H), 1.76-1.87 (m, 2H), 1.34-1.45 (m, 2H), 0.82-0.96 (m,6H).

Example 4 N-(1-isoproply-1H-indazol-6-yl)butane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.97 (s, 1H), 7.67 (d, J==8.54 Hz, 1H), 7.43(s, 1H), 6.86 (dd, J=1.83, 8.54 Hz, 1H), 6.63 (s, 1H), 4.80 (td, J=6.60,13.35 Hz, 1H), 3.03-3.20 (m, 2H), 1.72-1.92 (m, 2H), 1.58 (d, J=6.41 Hz,6H+1H from H2O), 1.31-1.51 (m, 2H), 0.90 (t, J=7.32 Hz, 3H).

Example 5 N-(1-phenyl-1H-1indazol-6-yl)butane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 8.17 (s, 1H), 7.75 (d, J=8.55 Hz, 1H),7.65-7.73 (m, 3H), 7.55 (t, J=7.93 Hz, 2H), 7.33-7.42 (m, 1H), 7.02 (dd,J=1.68, 8.70 Hz, 1H), 6.70 (s, 1H), 3.06-3.17 (m, 2H), 1.76-1.87 (m,2H), 1.34-1.45 (m, 2H), 0.89 (t, J=7.32 Hz, 3H).

Example 6 N-(1-benzyl-1H-indazol-6-yl)butane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 8.00 (s, 1H), 7.67 (d, J=8.54 Hz, 1H),7.14-7.43 (m, 5H), 6.87 (d, J=8.54 Hz, 1H), 6.60 (s, 1H), 5.57 (s, 2H),2.92-3.11 (m, 2H), 1.74 (t, J=7.63 Hz, 2H), 1.28-1.43 (m, 2H), 0.85 (t,J=7.32 Hz, 3H).

Example 7 N-(1-methyl-1-indazol-6-yl)methanesulfonamide

¹H NMR (500 MHz, CD3OD) δ 7.94 (s, 1H), 7.70 (d, J=8.5 Hz, 1H), 7.41 (s,1H), 7.03 (d, J=8.5 Hz, 1H), 4.02 (s, 3H), 3.00 (s, 3H).

Example 8 N-(1-methyl-1H-indazol-6-yl)ethanesulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.94 (br s, 1H), 7.67 (d, J=7.93 Hz, 1H), 7.39(br s, 1H), 6.96 (br s, 1H), 6.91 (d, J=7.63 Hz, 1H), 4.05 (br s, 3H),3.04-3.27 (m, 2H), 1.29-1.47 (m, 3H).

Example 9 N-(1-methyl-1H-indazol-6-yl)propane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.94 (s, 1H), 7.67 (d, J=8.5 Hz, 1H), 7.39 (s,1H), 6.86 (d, J=8.5 Hz, 1H), 6.61 (s, 1H), 4.06 (s, 3H), 3.06-3.15 (m,2H), 1.88 (qd, J=7.5, 15.3 Hz, 2H), 1.02 (t, J=7.3 Hz, 3H).

Example 10 N-(1-methyl-1H-indazol-6-yl)propane-2-sulfonamide

¹H NMR (500 MHz, Acetone) δ 8.75 (br s, 1H), 7.90 (s, 1H), 7.70 (d,J=8.54 Hz, 1H), 7.51 (s, 1H), 7.16 (dd, J=1.68, 8.70 Hz, 1H), 4.01 (s,3H), 3.37 (1d, J=6.75, 13.66 Hz, 1H), 1.33 (d, J=7.02 Hz, 6H).

Example 11 N-(1-methyl-1H-indazol-6-yl)pentane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.94 (s, 1H), 7.67 (d, J=8.5 Hz, 1H), 7.39 (s,1H), 6.88 (d, J=8.5 Hz, 1H), 6.77 (br s, 1H), 4.06 (s, 3H), 3.08-3.15(m, 2H), 1.84 (quint, J=7.7 Hz, 2H), 1.23-1.40 (m, 4H), 0.86 (t, J=7.2Hz, 3H).

Example 12 N-(1-methyl-1H-Indazol-6-yl)hexane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.95 (s, 1H), 7.67 (d, J=8.54 Hz, 1H), 7.39(s, 1H), 6.88 (d, J=8.24 Hz, 1H), 6.81 (br s, 1H), 4.06 (s, 3H),3.06-3.16 (m, 2H), 1.78-1.89 (m, 2H), 1.31-1.42 (m, 2H), 1.24 (br s, 2H+grease), 0.81-0.87 (m, 3H).

Example 13 4-cyano-N-(1-methyl-1H-indazol-6-yl)butane-1-sulfonamide

¹H NMR. (500 MHz, CDCl3) δ 7.95 (s, 1H), 7.69 (d, J=8.5 Hz, 1H), 7.39(s, 1H), 6.91 (d, J=8.2 Hz, 1H), 6.80 (s, 1H), 4.06 (s, 3H), 3.17 (t,J=7.3 Hz, 2H), 2.38 (t, J=6.9 Hz, 2H), 2.02 (quin, J=7.5 Hz, 2H),1.75-1.86 (m, 2H).

Example 14 4-methoxy-N-(1-methyl-1H-indazol-6-yl)butane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.94 (s, 1H), 7.67 (d, J=8.5 Hz, 1H), 7.39 (s,1H), 6.88 (d, J=8.2 Hz, 1H), 6.84 (br s, 1H), 4.06 (s, 3H), 3.34 (t,J=5.5 Hz, 2H), 3.26 (s, 3H), 3.17 (t, J=7.5 Hz, 2H), 1.94 (quin, J=7.4Hz, 2H), 1.59-1.68 (m, 2H).

Example 155-methoxy-3-methyl-N-(1-methy-1l-indazol-6-yl)pentane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.94 (s, 1H), 7.66 (d, J=8.54 Hz, 1H), 7.39(s, 1H), 7.19 (br s, 1H), 6.91 (dd, J=1.83, 8.54 Hz, 1H), 4.05 (s, 3H),3.29-3.40 (m, 2H), 3.25 (s, 3H), 3.07-3.20 (m, 2H), 1.89 (ddd, J=5.49,7.78, 10.83 Hz, 1H), 1.62-1.73 (m, 2H), 1.47-1.57 (m, 1H), 1.31-1.42 (m,1H), 0.85 (d, J=6.41 Hz, 3H).

Example 16 N-(1-methyl-1H-indazol-6-yl)hexane-3-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.93 (s, 1H), 7.06 (d, J=8.5 Hz, 1H), 7.39 (s,1H), 6.85 (dd, J=1.83, 8.5 Hz, 1H), 6.57 (br s, 1H), 4.05 (s, 3H), 3.02(quin, J=5.8 Hz, 1H), 1.74-1.98 (m, 4H), 1.45-1.57 (m, 1H), 1.33-1.45(m, 1H), 1.03 (t, J=7.5 Hz, 3H), 0.89 (t, J=7.3 Hz, 3H).

Example 17 N-(1-methyl-1H-indazol-6-yl)pentane-2-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.93 (s, 1H), 7.66 (d, J=8.5 Hz, 1H), 7.39 (s,1H), 6.89 (d, J=8.5 Hz, 1H), 6.78 (s, 1H), 4.05 (s, 3H), 3.12-3.24 (m,1H), 1.92-2.06 (m, 1H), 1.56-1.69 (m, 1H), 1.46-1.56 (m, 1H), 1.36-1.42(m, 3H), 1.25-1.35 (m, 1H), 0.89 (t, J=7.3 Hz, 3H).

Example 18 4-methyl-N-(1-methyl-1H-indazol-6-yl)pentane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.94 (s, 1H), 7.67 (d, J=8.54 Hz, 1H), 7.39(s, 1H), 6.87 (dd, J=1.68, 8.70 Hz, 1H), 6.76 (br s, 1H), 4.06 (s, 3H),3.01-3.14 (m, 2H), 1.76-1.90 (m, 2H), 1.51 (quind, J=6.64, 13.41 Hz,1H), 1.22-1.29 (m, 2H), 0.85 (d, J=6.41 Hz, 6H).

Example 19 4-methyl-N-(1-methyl-1K-indazol-6-yl)benzenesulfonamide

¹H NMR (500 MHz, CD3OD) δ 7.87 (br s, 1H), 7.67 (d, J=6.4 Hz, 2H), 7.56(d, J=8.5 Hz, 1H), 7.23-7.31 (m, 3H), 6.86 (d, J=8.5 Hz, 1H), 3.95 (brs, 3H), 2.34 (br s, 3H).

Example 20 N-(1-methyl-1H-indazol-6-yl)-1-phenylmethanesulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.93 (s, 1H), 7.62-7.73 (m, 1H), 7.27-7.41 (m,5H), 6.72 (d, J=8.5 Hz, 1H), 6.57 (br s, 1H), 4.38 (s, 2H), 4.03 (s,3H).

Example 21 N-(1-methyl-1H-indazol-6-yl)-2-phenylethane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.93 (s, 1H), 7.62 (d, J=8.5 Hz, 1H),7.26-7.33 (m, 3H), 7.20 (s, 1H), 7.15 (d, J=7.3 Hz, 2H), 6.65 (d, J=8.5Hz, 1H), 6.42 (s, 1H), 4.04 (s, 3H), 3.39 (t, J=7.6 Hz, 2H), 3.16 (t,J=7.6 Hz, 2H).

Example 22 N-(1-methyl-1H-indazol-6-yl)cyclopropanesulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.95 (s, 1H), 7.67 (d, J=8.5 Hz, 1H), 7.41 (s,1H), 6.95 (dd, J=1.9, 8.4 Hz, 1H), 6.60 (s, 1H), 4.06 (s, 3H), 2.46-2.59(m, 1H), 1.16-1.23 (m, 2H), 0.91-1.01 (m, 2H).

Example 23 N-(1-methyl-1H-indazol-6-yl)cyclobutanesulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.93 (s, 1H), 7.65 (d, J=8.54 Hz, 1H), 7.37(s, 1H), 6.86 (d, J=8.55 Hz, 1H), 6.75 (br s, 1H), 4.05 (s, 3H), 3.94(quin, J=8.32 Hz, 1H), 2.52-2.63 (m, 2H), 2.20-2.30 (m, 2H), 1.91-2.05(m, 2H).

Example 24 N-(1-methyl-1H-indazol-6-yl)cyclopentanesulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.93 (s, 1H), 7.66 (d, J=8.24 Hz, 1H), 7.41(s, 1H), 6.87 (d, J=8.54 Hz, 1H), 6.54 (s, 1H), 4.05 (s, 3H), 3.50-3.62(m, 1H), 1.93-2.14 (m, 5H), 1.78-1.87 (m, 2H), 1.58-1.64 (m, 2H).

Example 25 N-(1-methyl-1H-indazol-6-yl)cyclohexanesulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.93 (s, 1H), 7.66 (d, J=8.54 Hz, 1H), 7.40(s, 1H), 6.86 (d, J=8.54 Hz, 1H), 6.52 (s, 1H), 4.05 (s, 3H), 2.97-3.11(m, 1H), 2.17 (d, J=12.82 Hz, 2H), 1.82-1.91 (m, 2H), 1.58-1.70 (m, 3H),1.14-1.23 (m, 3H).

Example 26N-(1-methyl-1H-indazol-6-yl)-4-(trifluoromethyl)cyclohexane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.94 (s, 1H), 7.67 (d, J=8.541 Hz, 1H), 7.39(s, 1H), 6.87 (dd, J=1.83, 8.54 Hz, 1H), 6.65 (s, 1H), 4.05 (s, 3H),3.22 (quin, J=5.57 Hz, 1H), 2.20-2.27 (m, 2H), 2.05-2.18 (m, 3H),1.82-1.93 (m, 2H), 1.67-1.75 (m, 2H).

Example 27 N-(1-methyl-1H-indazol-6-yl)piperidine-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.92 (s, 1H), 7.63 (d, J=8.54 Hz, 1H), 7.30(s, 1H), 7.01 (br s, 1H), 6.90 (dd, J=1.53, 8.54 Hz, 1H), 4.04 (s, 3H),3.21-3.31 (m, 4H), 1.50-1.57 (m, 4H), 1.43-1.50 (m, 2H).

Example 28 1-cyclohexyl-N-(1-methyl-1H-indazol-6-yl)methanesulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.94 (s, 1H), 7.67 (d, J=8.24 Hz, 1H), 7.37(s, 1H), 6.87 (d, J=8.54 Hz, 1H), 6.81 (s, 1H), 4.05 (s, 3H), 3.01 (d,J=6.10 Hz, 2H), 1.99-2.13 (m, 1H), 1.87-1.99 (m, J=12.50 Hz, 2H),1.64-1.75 (m, J=13.40 Hz, 2H), 1.21-1.36 (m, 2H), 0.98-1.21 (m, 3H).

Example 29 N-(1-(methyl-d3)-1H-indazol-6-yl)butane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.95 (s, 1H), 7.68 (d, J=8.5 Hz, 1H),7.37-7.44 (m, 1H), 6.89 (dd, J=2.14, 8.5 Hz, 1H), 6.80 (br s, 1H),3.10-3.17 (m, 2H), 1.78-1.87 (m, 2H), 1.41 (qd, J=7.5, 14.9 Hz, 2H),0.90 (t, J=7.3 Hz, 3H).

Example 30 N-(1-(methyl-d3)-1H-indazol-6-yl)pentane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.95 (s, 1H), 7.67 (d, J=8.5 Hz, 1H), 7.38 (s,1H), 6.87 (d, J=8.5 Hz, 1H), 6.70 (s, 1H), 3.06-3.17 (m, 2H), 1.84(quint, J=7.5 Hz, 2H), 1.22-1.42 (m, 4H), 0.86 (t, J=7.0 Hz, 3H).

Example 314-methoxy-N-(1-(methyl-d3)-1H-indazol-6-yl)butane-1-sulfonamide

¹H NMR (500 MHz, CDCl3) δ 7.94 (s, 1H), 7.67 (d, J=8.54 Hz, 1H), 7.38(s, 1H), 6.87 (d, J=8.54 Hz, 1H), 6.70 (br s, 1H), 3.35 (t, J=5.80 Hz,2H), 3.26 (s, 3H), 3.17 (t, J=7.48 Hz, 2H), 1.87-2.02 (m, 2H), 1.53-1.72(m, 2H+1H from H2O).

Example 32 Synthesis ofN-methyl-N-(1-methyl-1H-indazol-6-yl)butane-1-sulfonamide

To a vigorously stirring, ice cold solution ofN-(1-methyl-1H-indazol-6-yl)butane-1-sulfonamide (78.8 mg, 0.295 mmol)in dimethylformamide (3 mL), NaH (47.2 mg, 1.18 mmol) was added in fourportions. The reaction mixture was maintained at 0° C. for 30 min andthen warmed to room temperature. Iodomethane (73.5 μL, 1.18 mmol) wasadded dropwise to the reaction mixture and the reaction was stirred for16 hours. The reaction mixture was quenched with water and diluted withethyl acetate. The reaction mixture was transferred to a separatoryfunnel, washed with water three times and dried over anhydrous magnesiumsulfate. The reaction mixture was concentrated on a rotary evaporatorand the residue was purified by flash chromatography on silica usingethyl acetate as eluent to afford the product as a yellow solid (70 mg,85% yield): ¹H NMR (500 MHz, CDCl3) δ 7.97 (s, 1H), 7.72 (d, J=8.5 Hz,1H), 7.48 (s, 1H), 7.13 (d, J=8.5 Hz, 1H), 4.07 (s, 3H), 3.42 (s, 3H),2.96-3.06 (m, 2H), 1.82 (m, 2H), 1.42 (m, 2H), 0.92 (t, J=7.32 Hz, 3H).

Example 33 Synthesis of 1-Butyl-3-(1-methyl-1H-indazol-6-yl)thiourea

To a solution of 1-methyl-1H-indazol-6-amine (27 mg, 0.183 mmol) inpyridine (1 mL), was added n-butylisothiocyanate (25 μL, 0.2 mmol) andthe reaction was stirred at room temperature for 14 h. After completionof the reaction, the reaction mixture was diluted with ethyl acetate,transferred to a separatory funnel and washed with water, saturatedsodium bicarbonate solution, and brine. The organic layer was dried overanhydrous magnesium sulfate and concentrated via rotary evaporator. Thecrude product was purified by flash chromatography on silica gel(gradient: 0-70% ethyl acetate/hexanes) to obtain the product as a whitesolid (34.6 mg, 72% yield): ¹H NMR (500 MHz, CDCl3) δ 8.00 (s, 1H), 7.77(d, J=8.2 Hz, 2H), 6.98 (dd, J=1.2, 8.5 Hz, 1H), 6.05 (br s, 1H), 4.06(s, 3H), 3.60-3.69 (m, 2H), 1.50-1.60 (m, 2H), 1.33 (qd, J=7.4, 15.0 Hz,2H), 0.92 (t, J=7.3 Hz, 3H).

Example 34 Synthesis of 1-Butyl-3-(1-methyl-1H-indazol-6-yl)urea

To a solution of I-methyl-1H-indazol-6-amine (30 mg, 0.204 mmol) inpyridine (1 mL), was added n-butylisocyanate (25.2 μL, 0.224 mmol) andthe reaction was stirred at room temperature for 14 hours. Aftercompletion of the reaction, the reaction mixture was diluted with ethylacetate, transferred to a separatory funnel and washed with water,saturated sodium bicarbonate solution, and brine. The organic layer wasdried over anhydrous magnesium sulfate and concentrated in vacuo. Thecrude product was purified by flash chromatography on silica gel(gradient: 0-70% ethyl acetate/hexanes) to obtain the product as a whitesolid (49.7 mg, 98% yield): ¹H NMR (500 MHz, CDCl3) δ 7.88 (s, 1H), 7.78(s, 1H), 7.56 (dd, J=4.9, 7.9 Hz, 1H), 6.64-6.92 (m, 2H), 4.71-5.10 (m,1H), 3.99 (d, J=4.3 Hz, 3H), 3.22-3.33 (m, 2H), 1.44-1.56 (m, 2H),1.29-1.41 (m, 2H), 0.83-0.99 (m, 3H).

Example 35 Synthesis of N-(1-methyl-1H-indazol-6-yl)propionamide

Using a procedure similar to that described in Example 36, the titlecompound was prepared: ¹H NMR (504) MHz, CDCl3) δ 8.19 (br s, 1H), 7.88(s, 1H), 7.78 (m, 1H), 7.57 (d, J=8.54 Hz, 1H), 6.83 (d, J=8.54 Hz, 1H),3.99 (s, 3H), 2.44 (q, J=7.32 Hz, 2H), 1.26 (t, J=7.48 Hz, 3H).

Example 36 Synthesis of N-(1-methyl-1H-indazol-6-yl)pentanamide

To a solution of 1-methyl-1H-indazol-6-amine (19 mg, 0.13 mmol) indichloromethane (1 mL) was added triethylamine (20 μL, 0.142 mmol). Tothis mixture, pentanoyl chloride (17 μL, 0.142 mmol) was added dropwiseat 0° C. The reaction was allowed to warm to room temperature and wasthen stirred for 16 hours. After completion of the reaction, thereaction mixture was diluted with ethyl acetate and transferred to aseparatory funnel. The organic layer was washed with saturated aqueoussodium bicarbonate solution, followed by water, and brine. The organiclayer was dried over anhydrous magnesium sulfate, filtered andconcentrated in vacuo. The crude product was purified by flashchromatography on silica gel (gradient: 0-70% ethyl acetate/hexanes) toobtain the product as a white solid (22.5 mg, 75% yield): ¹H NMR (50)MHz, d6-acetone) δ 9.26 (br s, 1H), 8.24 (s, 1H), 7.84 (s, 1H), 7.61 (d,J=8.5 Hz, 1H), 7.08 (dd, J=1.7, 8.7 Hz, 1H), 4.00 (s, 3H), 2.41 (t,J=7.48 Hz, 2H), 1.68 (quin, J=7.55 Hz, 2H), 1.40 (qd, J=7.4, 14.9 Hz,2H), 0.93 (t, J=7.5 Hz, 3H).

Example 37 Synthesis of Ethyl (1-methyl-1H-indazol-6-yl)carbamate

To a solution of 1-methyl-1H-indazol-6-amine (35.6 mg, 0.241 mmol) indichloromethane (2 mL) was added triethylamine (36.8 μL, 0.264 mmol).Ethyl chloroformate (25.3 μL, 0.264 mmol) was then added dropwise at 0°C. and the reaction was allowed to warm to room temperature. After 16hours, the reaction mixture was diluted with ethyl acetate andtransferred to a separatory funnel. The organic layer was washed withsaturated aqueous sodium bicarbonate solution, followed by water, andbrine. The organic layer was dried over anhydrous magnesium sulfate,filtered and concentrated in vacuo. The crude product was purified byflash chromatography on silica gel (gradient: 0-70% ethylacetate/hexanes) to obtain the product as a white solid (28.3 mg, 54%yield): ¹H NMR (500 MHz, CDCl3) δ 7.89 (s, 2), 7.59 (d, J=8.5 Hz, 1H),6.73-6.83 (m, 2H), 4.27 (q, J=7.0 Hz, 2H), 4.03 (s, 3H), 1.34 (t, J=7.2Hz, 3H).

Example 38 Synthesis of n-propyl(1-methyl-1H-indazol-6-yl)carbamate

Using a procedure similar to that described in Example 39, the titlecompound was prepared (24.2 mg, 76% yield): ¹H NMR (500 MHz, CDCl3) δ7.89 (s, 1H), 7.59 (d, J=8.54 Hz, 1H), 6.78 (dd, J=1.53, 8.54 Hz, 2H),4.17 (t, J=6.71 Hz, 2H), 4.03 (s, 3H), 1.73 (sxt, J=7.14 Hz, 2H), 1.00(t, J=7.32 Hz, 3H).

Example 39 Synthesis of Butyl (1-methyl-1H-indazol-6-yl)carbamate

A solution of 1-methyl-1H-indazol-6-amine (12.5 mg, 0.084 mmol) and1,1′-carbonyldiimidazole (15.0 mg, 0.093 mmol) in dichloromethane (1 mL)was stirred under reflux conditions for 4 hours. After the startingmaterial was consumed, n-butanol (1 mL) was added and the reaction wasrefluxed for an additional 12 h. After completion of the reaction, thereaction mixture was concentrated in vacuo. The crude product waspurified by flash chromatography on silica gel (gradient: 0-70% ethylacetate/hexanes) to afford the product as a white solid (16.5 mg, 79%yield): ¹H NMR (500 MHz, CDCl3) δ 7.82 (s, 1H), 7.53 (d, J=8.54 Hz, 1H),6.65-6.74 (m, 2H), 4.14 (t, J=6.56 Hz, 2H), 3.96 (s, 3H), 1.50-1.68 (m,2H+H from H2O), 1.38 (qd, J=7.40, 15.03 Hz, 2H), 0.90 (t, J=7.32 Hz,3H).

Example 40 Synthesis of 1-Methyl-N-pentyl-1H-indazol-6-amine

To a solution of 36 (FIG. 7, 14.4 mg, 0.06 mmol) in tetrahydrofuran (0.5mL) was added lithium aluminum hydride (0.12 mL of 1 M solution intetrahydrofuran, 0.12 mmol) dropwise at 0° C. The reaction was allowedto warm to room temperature and was then stirred for 16 hours. Aftercompletion of the reaction, the reaction mixture was diluted with ethylacetate and transferred to a separatory funnel. The organic layer waswashed with saturated aqueous sodium bicarbonate solution, followed bywater, and brine. The organic layer was dried over anhydrous magnesiumsulfate, filtered and concentrated. The crude product was purified byflash chromatography on silica gel (gradient: 0-70% ethylacetate/hexanes) to obtain the product as a white solid (12.4 mg, 95%yield): ¹H NMR (500 MHz, CDCl3) δ 7.76 (s, 1H), 7.43 (d, J=8.54 Hz, 1H),6.48 (dd, J=1.83, 8.85 Hz, 1H), 6.30 (s, 1H), 3.95 (s, 3H), 3.17 (t,J=7.17 Hz, 2H), 1.69 (quin, J=7.17 Hz, 2H), 1.31-1.49 (m, 4H), 0.94 (t,J=7.02 Hz, 3H).

Example 41 Synthesis of N-(3-methyl-1H-indazol-5-yl)butane-1-sulfonamide

To a solution of 4 h (FIG. 7, 30 mg, 0.20 mmol) in pyridine (1 mL) wasadded n-butyl sulfonyl chloride (29 μL, 0.22 mmol) and the reaction wasstirred at room temperature for 16 hours. After completion of thereaction, the reaction mixture was diluted with ethyl acetate andtransferred to a separatory funnel. The organic layer was washed withsaturated aqueous sodium bicarbonate solution, followed by water, andbrine. The organic layer was dried over anhydrous magnesium sulfate,filtered and concentrated. The crude product was purified by flashchromatography on silica gel (gradient: 30-70% ethyl acetate/hexanes) toobtain the product as a white solid (36.8 mg, 69% yield): ¹H NMR (500MHz, CDCl₃) δ 7.60 (s, 1), 7.44 (d, J=8.85 Hz, 1), 7.28 (s, 1), 6.43 (brs, 1), 2.95-3.14 (m, 2), 2.60 (s, 3), 1.77-1.90 (m, 1), 1.35-1.53 (m,2), 0.91 (t, J=7.32 Hz, 3).

Examples 42-53

Using procedures similar to those described herein, the followingrepresentative compounds of the invention were also prepared.

Example 42 Synthesis ofN-(3-methyl-1H-indazol-5-yl)pentane-1-sulfonamide

Using a procedure similar to that described in Example 41, the titlecompound was prepared: ¹H NMR (500 MHz, CDCl₃) δ 7.59 (s, 1H), 7.42 (d,J=8.5 Hz, 1H), 7.28 (br s, 1H+CDCl₃), 6.70 (s, 1H), 2.99-3.11 (m, 2H),2.59 (s, 3H), 1.80-1.93 (m, 2H), 1.19-1.42 (m, 4H), 0.87 (t, J=5.9 Hz,3H).

Example 43 Synthesis of4-Fluoro-N-(3-methyl-1H-indazol-5-yl)butane-1-sulfonamide

The following scheme illustrates the synthesis of Examples 43 and 45.

a. Preparation of:

5-Nitro-3-methyl-1H-indazole (1.03 g, 5.81 mmol; Synthonix) was placedinto an oven-dried round bottom flask, followed by the 10% Pd/C (0.1 wt%; Sigma Aldrich). The reagents were suspended in 30 mL of anhydrousethanol (Fisher Scientific) and equipped with a balloon with H2. Thereaction proceeded for 64 h at room temperature, after which thereaction was filtered and concentrated to yield5-amino-3-methyl-1H-indazole as a tan solid (658 mg, 77% yield). Thereaction product was judged satisfactory by LC-MS and used without ¹HNMR characterization.

b. Preparation of:

5-Amino-3-methyl-1H-indazole (658 mg, 4.48 mmol) was placed into anoven-dried round bottom flask, and suspended in 30 mL of anhydrouspyridine (Sigma Aldrich). The mixture was cooled down to 0° C. and then4-fluorobutanesulfonyl chloride (742 mg, 4.25 mmol; Enamine) was addeddropwise by syringe. The reaction was allowed to proceed overnight,after which it was concentrated into a dark burgundy residue. Theresidue was suspended in ethyl acetate and 0.1 N HCl_((aq)), extractedthree times with ethyl acetate and washed with brine. The organicfraction was harvested, dried over Na₂SO₄ (Fisher Scientific), andfinally concentrated. The product was purified by flash columnchromatography (40 g column, 0%→100% ethyl acetate:hexanes). The titlecompound was obtained as an off-white solid (1.02 g, 85% yield).[M+H]⁺=286.0. ¹H NMR (500 MHz, d₆-DMSO) δ 12.64 (s, 1), 9.58 (s, 1),7.48 (d, J=1.4 Hz, 1), 7.43 (d, J=8.8 Hz, 1), 7.22 (dd, J=8.8, 1.7 Hz,1), 4.47 (t, J=5.5 Hz, 1), 4.37 (t, J=5.8 Hz, 1), 3.10-3.01 (m, 2), 2.45(s, 3), 1.83-1.66 (m, 4).

Example 44 Synthesis of4,4-trifluoro-N-(3-methyl-1H-indazol-5-yl)butane-1-sulfonamide

Using a procedure similar to that described in Example 41, the titlecompound was prepared: ¹H NMR (500 MHz, MeOD) δ 7.58 (d, J=1.2 Hz, 1H),7.45 (d, J=8.8 Hz, 1H), 7.31 (dd, J=8.8, 1.8 Hz, 1H), 3.14 (t, J=7.6 Hz,2H), 2.53 (s, 3H), 2.23-2.43 (m, 2H), 1.95-2.11 (m, 2H).

Synthesis of 3-chloro-1H-indazol-5-amine (10)

To a solution of 2-methyl-4-nitroaniline (298 mg, 1.96 mmol), in aceticacid maintained at 0° C. was added dropwise sodium nitrite (135.2 mg,1.96 mmol) dissolved in water. The reaction was stirred at roomtemperature for 72 h. The reaction mixture was concentrated on rotaryevaporator and the residue was diluted with ethyl acetate and washedwith saturated aqueous sodium bicarbonate solution and brine. Theorganic layer was dried over anhydrous magnesium sulfate, filtered, andconcentrated in vacuo to yield 5-nitro-1H-indazole (6) in quantitativeyield.

To a solution of sodium hydroxide (274 g, 6.84 mmol) in H.2O (8 mL) wasadded 5-nitroindazole (6)(280 mg, 1.71 mmol), and the mixture was heateduntil a red solution formed. The mixture was cooled in an ice-water bathfor 15 minutes, sodium hypochlorite (3.3 mL, 5.25%, 2.5 mmol) was addedand the mixture stirred at 0° C. for 12 h after which the pH wasadjusted to 7 with diluted HCL. The mixture was extracted with ethylacetate, and the combined organic layer washed with water andconcentrated under reduced pressure. The residue was purified by flashchromatography to provide 3-chloro-5-nitro-1H-indazole (7) (310 mg, 92%yield), m/z 198 [M+H]⁺.

To a solution of 3-chloro-5-nitro-1H-indazole (7)(310 mg, 1.57 mmol) inethanol (150 mL) was added stannous chloride dihydrate (1.77 g, 7.85mmol). The reaction mixture was refluxed for 4 h. After completion ofreaction, the mixture was concentrated on rotary evaporator. The residuewas diluted with dichloromethane and basified with sodium hydroxide. Themixture was transferred to separatory funnel and the aqueous layer wasextracted with dichloromethane The combined organic layer was dried overanhydrous magnesium sulfate, filtered, and concentrated in vacuo. Theresidue was purified by flash chromatography to provide3-chloro-1H-indazol-5-amine (10) (186 mg, 71 yield), m/z 168 [M+H]⁺.

Example 45 Synthesis of N-(3-chloro-1H-indazol-5-yl)butane-1-sulfonamide

a. Preparation of:

3-Chloro-5-nitro-1H-indazole (800 mg, 4.06 mmol; Combi-Blocks) wasplaced into an oven-dried round bottom flask, followed by the additionof stannous chloride dehydrate (4.50 g, 20.0 mmol; Acros Organics). Thereaction mixture was suspended in 40 mL of anhydrous ethanol andproceeded overnight at room temperature. The mixture was thenconcentrated, extracted three times with ethyl acetate and washed oncewith brine. The organic layer was dried over Na₂SO₄, filtered and thenconcentrated to yield 5-amino-3-chloro-1H-indazole as an off-white solid(644 mg, 95% yield). The reaction product was judged satisfactory byLC-MS and used without ¹H NMR characterization.

b. Preparation of:

5-Amino-3-chloro-1H-indazole (644 mg, 3.86 mmol) was placed into anoven-dried round bottom flask, and suspended in 10 mL of anhydrouspyridine. The mixture was cooled down to 0° C. and then 1-butanesulfonylchloride (498 μL, 3.86 mmol; Enamine) was added dropwise by syringe. Thereaction proceeded overnight after which it was concentrated, extractedthree times with ethyl acetate, washed once with brine, and dried overNa₂SO₄. The organic layer was concentrated and purified by flash columnchromatography (40 g column, 0% to 100% ethyl acetate:hexanes). Thetitle compound was obtained as a white solid (307 mg, 28% yield).[M+H]⁺=288.0. ¹H NMR (500 MHz, CDCl₃) δ 10.0 (br s, 1H), 7.56 (br s,1H), 7.45 (d, J=8.5 Hz, 1H), 7.38 (d, J=8.5 Hz, 1H), 6.55 (br s, 1H),3.02-3.15 (m, 2H), 1.77-1.89 (m, 2H), 1.36-1.49 (m, 2H), 0.92 (t, J=6.7Hz, 3H).

Example 46 Synthesis ofN-(3-chloro-1H-indazol-5-yl)pentane-1-sulfonamide

Using a procedure similar to that described in Example 45, the titlecompound was prepared: ¹H NMR (500 MHz, CDCl₃) δ 10.1 (br s, 1H), 7.57(s, 1H), 7.46 (d, J=8.8 Hz, 1H), 7.39 (d, J=8.8 Hz, 1H), 6.62 (s, 1H),2.94-3.16 (m, 2H), 1.86 (quin, J=7.6 Hz, 2H), 1.28-1.42 (m, 4H), 0.88(t, J=7.2 Hz, 3H)

Example 47 Synthesis ofN-(3-chloro-1H-indazol-5-yl)-4-fluorobutane-1-sulfonamide

Using a procedure similar to that described in Example 45, the titlecompound was prepared: ¹H NMR (500 MHz, CDCl₃) δ 9.94 (br s, 1H), 7.58(s, 1H), 7.47 (d, J=8.8 Hz, 1H), 7.39 (dd, J=2.1, 8.8 Hz, 1H), 6.47 (s,1H), 4.47-4.56 (m, 1H), 4.37-4.45 (m, 1H), 3.11-3.21 (m, 2H), 2.03 (td,J=7.5, 15.4 Hz, 2H), 1.76-1.92 (m, 2H)

Example 48 Synthesis ofN-(3-chloro-1H-indazol-5-yl)-4,4,4-trifluorobutane-1-sulfonamide

Using a procedure similar to that described in Example 45, the titlecompound was prepared: ¹H NMR (500 MHz, CDCl₃) δ 9.92 (br s, 1H), 7.58(s, 1H), 7.48 (d, J=9.2 Hz, 1H), 7.35-7.40 (m, 1H), 6.43 (br s, 1H),3.17 (t, J=7.5 Hz, 2H), 2.23-2.45 (m, 2H), 2.15 (quin, J=7.5 Hz, 2H).

Example 49 Synthesis ofN-(3-chloro-6-methyl-1H-indazol-5-yl)butane-1-sulfonamide

Using a procedure similar to that described in Example 45, the titlecompound was prepared: ¹H NMR (500 MHz, CDCl₃) δ 9.79 (br s, 1H), 7.70(s, 1H), 7.33 (s, 1H), 6.06 (s, 1H), 3.06-3.24 (m, 2H), 2.49 (s, 3H),1.79-1.98 (m, 2H), 1.41-1.52 (m, 2H), 0.95 (t, J=7.3 Hz, 3H).

Example 50 Synthesis ofN-(3-chloro-6-methyl-1H-indazol-5-yl)-4-fluorobutane-1-sulfonamide

Using a procedure similar to that described in Example 45, the titlecompound was prepared: ¹H NMR (500 MHz, CDCl₃) δ 9.82 (br s, 1H), 7.70(s, 1H), 7.33 (s, 1H), 6.12 (s, 1H), 4.53 (t, J=5.6 Hz, 1H), 4.44 (t,J=5.6 Hz, 1H), 3.16-3.32 (m, 2H), 2.06 (td, J=15.3, 7.6, Hz, 2H),1.75-1.97 (m, 2H).

Example 51 Synthesis ofN-(3-trifluoromethyl-1H-indazol-5-yl)butane-1-sulfonamide

Using a procedure similar to that described in Example 45, the titlecompound was prepared: ¹H NMR (500 MHz, CDCl₃) δ 10.4 (br s, 1), 7.66(s, 1), 7.58 (d, J=9.2 Hz, 1), 7.49 (dd, J=9.0, 1.7, Hz, 1), 6.41 (s,1), 3.01-3.19 (m, 2), 1.77-1.92 (m, 2), 1.44 (qd, J=14.9, 7.4 Hz, 2),0.92 (t, J=7.5 Hz, 3).

Example 52 Synthesis ofN-(3-trifluoromethyl-1H-indazol-5-yl)pentane-1-sulfonamide

Using a procedure similar to that described in Example 45, the titlecompound was prepared: ¹H NMR (500 MHz, CDCl3) δ 10.7 (br s, 1), 7.67(s, 1), 7.58 (d, J=9.2 Hz, 1), 7.49 (dd, J=8.8, 1.8 Hz, 1), 6.75 (br s,1), 3.05-3.16 (m, 2), 1.86 (td, J=15.5, 7.8 Hz, 2), 1.26-1.43 (m, 4),0.87 (t, J=7.2 Hz, 3).

Example 53 Synthesis ofN-(7-fluoro-3-methyl-1H-indazol-5-yl)-4-fluorobutane-1-sulfonamide

Using a procedure similar to that described in Example 45, the titlecompound was prepared: ¹H NMR (500 MHz, d₆-DMSO) δ 13.2 (br s, 1), 9.75(s, 1), 7.31 (s, 1), 7.06 (d, J=12.5 Hz, 1), 4.46 (t, J=10.5 Hz, 1),4.37 (t, J=11.5 Hz, 1), 3.11 (t, J=0.15 Hz, 2), 2.46 (s, 3), 1.78 (q,J=17.5 Hz, 3), 1.69 (t, J=13.5 Hz, 1).

Example 54 Biological Data

DG167 is an Inhibitor of M. tuberculosis KasA.

A library of 168 compounds with established antitubercular whole-cellefficacy for putative cell-wall inhibitors was screened using apreviously described M. bovis BCG strain harboring a lacZ reporter fusedto the M. tuberculosis iniBAC promoter (PiniBA) (Alland et al., 2000;Tahlan et al., 2012; Wilson et al., 2013). GSK3011724_(A). (Ballell, L.,et al., Chem Med Chem, 2013, 8, 313-321) (renamed DG167) was found to beone of the top inducers of iniBAC promoter (approximately 12 fold),suggesting that DG167 was likely to inhibit a component of cell-wallbiosynthesis. DG167 possessed potent whole-cell activity against M.tuberculosis with a minimum inhibitory concentration (MIC₉₀) of 0.39 μM.Activity was preserved against both drug-susceptible and drug-resistantclinical M. tuberculosis strains and against M. tuberculosis strainsresistant to MmpL3 inhibitors such as SQ109 suggesting a novel targetfor DG167 (Table 1, FIG. 1). Interestingly, DG167 lacked whole-cellactivity (MIC>100 μM) against nontuberculous mycobacteria (NTMs) such asM, abscessus, M. fortuitum, M. avium, M. smegmatis and M. marinum (Table1). DG167-resistant M. tuberculosis mutants were selected to gaininsights into its molecular target. All seven DG167-resistant mutantsanalyzed (MIC shift of 4 to >256×) remained susceptible to INH, EMB,ETH, rifampicin (Rif), moxifloxacin (Moxi), PA824, SQ109, and BDQ (Table2, FIG. 2). Whole-genome sequencing (WGS) of each mutant identified aunique single-nucleotide polymorphism (SNP) in the M. tuberculosis kasAgene (Table 2). Computational docking studies with the known KasAstructure (Luckner, S. R., et al., Structure, 2009, 17, 1004-1013) wereperformed, and DG167 was predicted to bind the KasA substrate-bindingsite.

KasA-DG167 Crystal Structure Reveals Unique Dual Binding to InteractingNonidentical Sites in the KasA Substrate-Binding Channel.

The X-ray crystal structure of KasA in complex with DG167 was solved togain insights into the DG167 mechanism of action.

M. tuberculosis KasA was overexpressed and purified from themycobacterial host M. smegmatis and the KasA-DG167 co-crystal structurewas refined to 2.00 Å resolution. The crystal structure of apo KasA,which was refined to 1.80 Å resolution using crystallization conditionssimilar to those used to crystallize KasA-DG167 was also determined.Each KasA monomer was found to bind to two DG167 molecules(KasA-DG167₂), with the result that the biological KasA dimer bound fourDG1167 molecules, i.e., KasA binds DG167_(A) and DG167_(B), and KasA′binds DG167_(A′) and DG167_(B). The clearly interpretable electrondensity corresponding to DG167_(A) and DG167_(B) showed the two DG167molecules bound to non-overlapping sites in the KasA acyl channelidentified as the phospholipid (PL) binding site observed in previouscrystal structures (Luckner, S. R., et al., Structure, 2009, 17,1004-1013). Consistent with the KasA-DG167₂ structure, the KasAmutations identified in the laboratory-generated DG1167-resistant M.tuberculosis strains mapped near the binding sites of both DG167_(A) andDG167_(B). Interestingly, the aliphatic moiety of DG167_(A) mimicsbinding of the PL acyl tail as it inserts into a pocket formed byresidues Gly200, Ile202, Pro206, Phe239, His345, and Ile347. TheDG167_(B) aliphatic moiety similarly follows the path traced by PL andpresumably bona fide acyl substrates (Luckner, S. R., et al., Structure,2009, 17, 1004-1013).

The DG167_(A) and DG167_(B) indazole groups make hydrophobicinteractions throughout the acyl channel and the DG167_(B) indazolegroup mediates additional hydrophobic contacts across the KasA/KasA′dimer interface. The KasA-DG167₂ interaction is further stabilized byhydrogen bonds between the DG167_(A) sulfonamide N—H and Glu199 (FIG.6A) as well as by the DG167_(B) indazole group nitrogen and a watermolecule coordinated by residues Gly115, Asn148, and Ala170 (FIGS. 6Aand 6B). Importantly, the two molecules of DG167 bound to the KasAmonomer form an intermolecular hydrogen bond. Specifically, a DG167_(A)sulfonamide oxygen hydrogen bonds with the DG167_(B) sulfonamide N—H(FIG. 68). In sum, an extensive array of both hydrophobic interactionsand hydrogen bonds stabilize the binding of two DG167 molecules to aKasA monomer. Moreover, the two DG167 molecules hydrogen bond to eachother and occupy the KasA surface that would otherwise bind theelongating acyl chain prior to the condensation reaction catalyzed byKasA. Thus, the KasA-DG167₂ co-crystal structure provides a plausiblemechanism by which DG167 can effectively compete for substrate binding,inhibit KasA activity, and produce a bactericidal effect on M.tuberculosis.

Biochemical Solution Studies and X-Ray Crystallographic Analysis Showthat Dual Inhibitor Binding is not Required to Disrupt KasA Function.

While two molecules of DG167 occupy the acyl channel, it washypothesized that a single compound bound to the channel would besufficient to block chain elongation. The X-ray crystal structure ofKasA in complex with Example 41 was determined, revealing that Example41 bound the acyl channel only once and in place of DG167_(A). It islikely that Example 41 cannot bind in place of DG167B because in asimilar pose the Example 41 indazole N(1)-H would be forced to interactwith a hydrophobic surface across the KasA dimer interface.

To measure the binding affinity of the DG167 and its analogs to KasA, amicroscale thermophoresis (MST) assay was developed. It was determinedthat the KasA-DG167 interaction has an EC₅₀=130.9±18.2 nM. Incomparison, Example 41 binds KasA tightly with a Kd=46.5±18.7 nM, whilean inactive des-methyl analog, Example 1, bound KasA very weakly with anEC₅₀=1736.1±221.2 nM). Consistent with the idea that a single compoundbound to the acyl channel is sufficient to block chain elongation,Example 41 displayed 2× improvement over DG167 in MIC against M.tuberculosis (MIC=0.20 μM, Table 3, FIG. 3).

DG167 inhibits mycolic acid biosynthesis. KasA is an essential componentof the FASII complex along with InhA. The effect of DG167 on mycolicacid biosynthesis was studied using a radiolabeled precursor,¹⁴C-acetate. DG167 exhibited dose-dependent inhibition of mycolic acidbiosynthesis (FIGS. 4A and 4C) like INH and inactive des-methyl analogExample 1 (Table 3) did not show any inhibition. Furthermore, aDG167-resistant isolate harboring KasA_(P206T) (DRM167-32x2, Table 2)was found to be resistant to DG167-mediated inhibition of mycolic acidbiosynthesis (FIGS. 4B and 4D). Additionally, inhibitors of FAS-II likesINH are known to cause accumulation of FAS-1 products and DG167treatment caused accumulation of C₁₆-C₂₆ short-chain fatty-acidsconfirming specific inhibition of FAS-II by DG167.

Synergistic Lethality of DG167 and INH.

INH treatment is known to induce high-level kasA expression in M.tuberculosis (Mdluli, K., et al., Science, 1998, e 280, 1607-1610; andVilcheze, C., et al., Nat Med, 2006, 12, 1027-1029) which couldpotentially antagonize the activity of DG167. However, a checkerboardassay revealed that DG167 and INH were additive (ΣPIC=1). Next, thebactericidal activity of DG167 and INH combination was evaluated. M.tuberculosis cultures (˜107 cells/mL) were treated with either 10× or20× the MIC of DG167, 10× the MIC of INH, or a combination of both drugsat 10× the MIC of each compound (FIG. 5A). DG167 alone reduced viablecolony-forming units (CFU) by 2 log 10 over seven days, and thisbactericidal effect was independent of the DG167 concentration tested.Treatment of the cultures with INH alone (10×MIC) resulted in rapidreduction of viable CFU followed by rapid re-growth. This typicalpattern of killing and regrowth has been previously attributed to theemergence of persisters combined with the emergence of INH resistantclones (Vilcheze, C., and Jacobs, W. R., Jr., Antimicrob AgentsChemother, 2012, 56, 5142-5148; and Wilson, R., et al., Nat Chem Biol,2013, 9, 499-506). Interestingly, the combined use of DG167 and INHmarkedly improved upon the bactericidal activity of either drug usedalone as it produced a rapid reduction in CFU, leading to completesterilization of these cultures. The synergistic lethality (Malik etal., 2014) observed upon treatment with the DG167-INH combinationsuggests that simultaneous inhibition of two essential FAS-II targets isstrongly bactericidal to M. tuberculosis, and that dual FAS-IIinhibition may overcome bacterial persistence.

Transcriptional profiling of M. tuberculosis treated with DG167 and INHreveals a unique signature that correlates with in vitro synergisticlethality. RNAseq analysis was performed to identify pathways that wereuniquely activated by dual treatment with DG167 and INH compared to thepathways activated by treatment with either drug alone. The goal was togain insights into the mechanisms underlying the synergistic lethalitythat was only observed after simultaneous treatment with both drugs.Single drug treatment with either INH or DG167 strongly inducedexpression of kasA, kasB, acpM genes, the iniBAC operon, andsignificantly altered the transcription of other genes known to bemodulated by INH (Alland. D., et al., Proc Natl Acad Sci USA, 1998, 95,13227-13232; Boshoff, H. I., et al., J Biol Chem, 2004, 279,40174-40184; and Vilcheze. C., and Jacobs, W. R., Jr., Microbiol Spectr,2014, 2, MGM2-0014-2013) (Table S2). With respect to the dual treatmentwith DG167 and INH, all but six of the genes that were differentiallyexpressed by DG167 treatment were also differentially expressed by INHtreatment, further supporting the hypothesis that DG167 and INH bothinhibit targets essential for the same biosynthetic pathway (FIG. 5B).As expected, dual treatment with DG167 and INH altered the expression ofalmost all (79) of the genes that were differentially expressed bytreatment with each drug alone. However, a surprisingly large number of54 additional genes were differentially expressed only in thedual-treated cultures (FIG. 5B). These “unique, dual-drug modulated”genes were not expressed in either of the cultures that were treatedwith DG167 or INH as mono-therapy; thus, the differential expression ofthese 54 genes correlated with synergistic lethality, i.e., a loss ofpersisters and culture sterilization rather than with drug exposure.Thirty-two of the unique dual-drug modulated genes were up-regulated.This set of up-regulated genes was enriched in oxidoreductases andputative transposase elements. Twenty-two of the unique dual-drugmodulated genes were down-regulated. This set of down-regulated geneswas enriched for chaperones (groEL1, groEL2 and groES), that aretypically up-regulated after treatment with bacteriostatic drugs(Belenky, P., et al., Cell Rep, 2015, 13, 968-980; Dwyer, D J., et al.,Mol Cell, 2002, 46, 561-572; and Lobritz, M. A., et al., Proc Natl AcadSci USA, 2015, 112, 8173-8180) and are also up-regulated in M.tuberculosis persisters during INH exposure (Jain et al., 2016).Together, these results strongly suggest that combined treatment withboth DG167 and INH activates a cellular response associated with loss ofpersistence and induction of cidality that is distinct from the cellularresponse induced by single drug treatment.

DG167 Profiling.

DG167 was profiled for desirable drug-like and pharmacokineticproperties. DG167 had good selectivity index (SI=CC50/MIC) of 59 withVero cells. The kinetic solubility in pH 7.4 phosphate-buffered saline(PBS) was 324 μM. The Caco-2 permeabilities (PA-B and PB-A) were71.8×10-6 and 45.6×10-6 cm/s, respectively. Cytochrome P450 (CYP)inhibition studies demonstrated DG167 did not significantly inhibit CYPenzymes except CYP2C19 (IC₅₀=12 μM), and hERG inhibition (IC₅₀>20 μM)was also ruled out. Mouse liver microsome (MLM) stability was suboptimalwith a t_(1/2)=10.1 min. However, the MLM t_(1/2) in the absence ofNADPH (to exclude oxidative metabolism) was >300 min. MLM-generatedmetabolites were examined through mass-spectrometry to identifymetabolic liabilities and improve MLM stability. A de-methylatedspecies, corresponding to loss of the 1-methyl group, predominated amongthe metabolites. When synthesized (Example 1), lacked activity againstM. tuberculosis (MIC>100 μM), suggesting a metabolic liability at aposition that is necessary for whole-cell activity. Promisingly, DG167accumulated in a dose-dependent manner in M. tuberculosis cells and thede-methylated form was not detected, indicating that DG167 is notinactivated by de-methylation inside the bacteria. The inactivedes-methyl analog (Example 1) also showed dose-dependent accumulationinside M. tuberculosis confirming that intact DG167 was essential fortarget inhibition and whole-cell activity (de Carvalho, et al., ACS MedChem Lett, 2011, 2, 849-854).

Synthesis of DG167 and Analogs.

The synthesis of DG167 and a focused series of analogs is depicted inFIG. 7. To address the primary metabolic stability of demethylation, aseries of N1-substituted indazoles was synthesized and evaluated foranti-tubercular activity and MLM stability. In comparison to DG167,longer or branched alkyl chains with the exception of an ethyl group atthe N1 position had unfavorable effects on both activity and MLMt_(1/2). The trideuteriomethyl analog Example 29 offered an improvementin metabolic stability (t_(1/2)=16.8 min). Since, Example 29 was a closeanalog of DG167, its co-crystal structure with KasA was also determined.It also exhibited a binary binding mode consistent with DG16. Analogsfeaturing replacement of the 6-position sulfonamide with functionalgroups like carbamate, amide, amine, and urea/thiourea, while retainingthe 1-N-methyl group, were synthesized and assayed. Amongst them only1-n-butyl-3-(1-methyl-1H-indazol-6-yl)thiourea (Example 33) demonstratedmodest activity (MIC=3.1 μM). N-methylation of the sulfonamide NH ofDG167 (Example 32) resulted in loss of activity. Based on the aboveresults, N1-methyl substitution and a 6-sulfonamide were identified assignificant elements for whole-cell efficacy. Subsequently, thesulfonamide n-butyl substituent was truncated or cyclized. Again, a lossof whole-cell activity was noted. Furthermore, the significant loss ofwhole-cell efficacy for analogs with branched alkyl sulfonamidesubstituents (i.e., Examples 15-18) hinted at the specific stericrequirements of the target enzyme binding site. While the n-hexylsulfonamide analog Example 12 was inactive, the elongation of n-butyl ton-pentyl chain at the R² position increased the activity over the parentby twofold when R¹=methyl (Example 11) as well as d3-methyl (Example30). Finally, the indazole's pyrazole unit was transposed to affordExample 41 that demonstrated a 2× improvement in whole-cell activity.

Mouse Pharmacokinetic Profile and Dose Tolerability.

PK profiling was performed to facilitate in vivo efficacy studies. ThePK profile of DG167 administered as a single oral dose of 25 mg/kgrevealed promising oral bioavailability (92.3%) and plasma levels(AUC0-t of 8083.96 h*ng/m. Plasma levels were maintained above the MICfor over 4 hours (FIG. 8). When IV dosed at 5 mg/kg, the half-life was0.33 h. A dose escalation study was performed at 50, 100, 250, and 500mg/kg where the mice were monitored for 8 hours. Both the 50 and 100mg/kg doses were well tolerated. At higher doses, the mice exhibitedheavy breathing, hunched posture and decreased activity. Dosetolerability studies performed for 5 d at 50 mg/kg, 100 mg/kg andcombination of DG167 (100 mg/kg) with INH (25 mg/kg) did not show anybehavioral changes or weight loss and normal liver pathology wasobserved (Table 4, FIG. 9).

DG167 and INH Exhibited In Vivo Synergy.

DG167 was studied in an acute murine infection model to determine itsefficacy against M. tuberculosis both alone and in combination with INH.INH is highly active against M. tuberculosis in the acute model,typically showing rapid clearance with 2 weeks of treatment. Therefore,treatment efficacy at the earlier (day 3 and day 7 post-treatment) timepoints was also studied. DG167 showed 99% reduction in bacterial burden(>2 log₁₀) over 2 weeks (FIG. 5C). Consistent with the in vitrobactericidal studies, the combined treatment of INH with DG167 produceda more rapid reduction in M. tuberculosis CFU than either INH or DG167alone during the two early time points. These data further emphasize thepotential benefits for treating TB with INH combined with and a KasAinhibitor.

Discussion

The results above demonstrate that DG167 inhibits mycolic acidbiosynthesis by targeting KasA, an essential member of the FAS-4lcomplex in M. tuberculosis. DG167 possessed in vitro activity comparableto INH and it targets the same cyclic pathway that produces long chainmycolic acids. Both INH and DG167 show similar three-phase kill curvesin vitro, characterized by an initial killing phase followed by aplateau in CFUs and finally outgrowth of both drug susceptible andresistant bacteria. Combined treatment with both INH and DG167eliminated the undesirable second and third phases and substantiallyenhanced bactericidal activity, leading to complete sterilization of thebacterial cultures. Synergistic lethality has been used to describe thesituation where two bacteriostatic drugs exhibit bactericidal propertieswhen used together (Malik, M., et al., J Antimicrob Chemother, 2014, 69,3227-3235). This term is also appropriate to describe the combinedeffect of DG167 and INH on M. tuberculosis (Jain, P., et al., MBio,2016, 7).

The results above suggest that dual treatment with DG167 and INH islikely to activate intrabacterial processes that could be associatedwith enhanced cidality. Transcriptional analysis revealed that theco-treatment differentially expressed a unique set of genes that werenot expressed by individual drug treatment. The pattern of genesdifferentially expressed by dual INH/DG167 treatment compared totreatment with either compound individually, including the induction ofoxidoreductases and nitrate reductase, and the suppression of molecularchaperones, suggests that dual treatment activates bactericidal andrepresses persistence mechanisms within the cell. This is supported bystudies in E. coli where bactericidal drugs develop common metabolicsignatures after the first 30 minutes of treatment such as elevation ofcentral carbon metabolites, breakdown of the nucleotide pool andelevated redox state, i.e., increases in respiration. This signaturediffers from a signature common to bacteriostatic drugs, e.g.,accumulation of metabolites that feed the electron transport chain andsuppress respiration (Belenky, P., et al., Cell Rep, 2015, 13, 98-980;and Lobritz, M. A., et al., Proc Natl Acad Sci USA, 2015, 112,8173-8180).

As described here and by others (Abrahams, K. A., et al., Nat Commun 7,2016, 12581). DG167 has a number of favorable PK-PD properties includinghigh potency, solubility, selectivity and low protein binding,suggesting that this molecule is a promising drug discovery lead.However, DG167 has relatively poor MLM stability, which requiresimprovement. Indeed, DG167 differs from other previously described KasAinhibitors such as TLM and its analogs (e.g., TLM5) that function bybinding to the KasA catalytic site. Instead, DG167 demonstrates a uniqueproperty for an antibacterial in that two DG167 molecules bind tonon-identical and non-overlapping surfaces of their target. Furthermore.DG167_(A) and DG167_(B) form an intermolecular hydrogen bond. It is alsoimportant to note that the KasA biological unit is a homo-dimer, and, asobserved in the crystal structure via the application ofcrystallographic symmetry, there are four molecules of DG167 bound perbiological KasA homo-dimer. DG167 binding stabilizes the KasA acylchannel flaps that are otherwise disordered in the absence of PL orDG167. In addition to interacting with their respective KasA, DG167_(B′)interacts with the KasA acyl channel flap, and DG167B interacts with theKasA acyl channel flap. Similarly, the KasA acyl channel flaps areordered in the KasA-Example 41 crystal structure, and Example 41 doesnot make contacts across the dimer interface. Thus, it seems that therequirement for KasA acyl channel flap stabilization is acyl channeloccupancy, and it seems likely that flap stabilization contributesallosterically to the binding of DG167 or Example 41 to KasA. Inaddition, while there are two bound DG167 molecules in the KasA-DG167₂structure, it is likely that the binding of either DG167 molecule wouldbe sufficient to block acyl chain elongation. This is supported by thefact that the DG167 analog Example 41 is an active inhibitor that bindsonly once to the acyl channel in a conformation similar to DG167_(A).

The results above also reveal other unique features of DG167, whichmight prove useful in the design of KasA inhibitors. In current models,acyl-AcpM drives a conformational change in Phe404 that not onlyactivates catalysis by triggering proton transfer from Cys171 to His311,but also permitting acyl chain access to the acyl channel and causingthe rearrangement of additional gatekeeper residues. In the KasA-DG167₂structure, Phe404 is in the closed conformation, i.e., acyl chain isexcluded from entering the channel. This is is believed to be the firsttime KasA was shown to bind ligand (e.g., inhibitor or PL) while Phe404is in the closed conformation. Moreover, it is clear that DG167 and acylchain could not bind simultaneously to KasA. Therefore, DG167 would bindpreferentially to non-acylated KasA, which distinguishes DG167 frompreviously identified KasA inhibitors that bind preferentially toacylated KasA. This is, in part, what makes DG167 unique from cellularfree fatty acids, which could, in theory, disrupt KasA functionsimilarly to DG167 if binding were promiscuous. While KasA has evolvedmechanisms to exclude free fatty acids from entering the acyl channelvia the phosphopantetheine tunnel and the surface near the disorderedflaps, DG167 circumvents the requirement for both AcpM and the openingof gatekeeper residue Phe404.

The conformational constraints and molecular interactions that governthe interactions between DG167 and KasA also suggest modifications thatcould either improve the potency or permit modifications that increasemetabolic stability of the current D3167 lead. In fact, the observed SARtrend of the initially synthesized analogs can be explained based on theKasADG167 crystal structure. Consistent with the two DG167 moleculesinteracting via a hydrogen bond formed between the sulfonamide oxygen onDG167A and the sulfonamide NH of DG167B, methylation of this nitrogen(Compound 33) resulted in a loss of activity. These substitutions forthe sulfonamide would also seem likely to significantly alter placementof the pendant alkyl chain. Carbamate, amide, amine, and urea % thioureafunctionalities at the 6-position of the indazole also disrupt thisintermolecular H-bonding interaction and lead to abrogation of activity.Truncation of the sulfonamide alkyl chain (Examples 7-9) or addingbulky/branched substituents (Example 10 and Examples 15-28) may disruptplacement of the acyl chain pocket formed by the residues Gly200,Ile202, Pro206, Phe239, His345, and Ile347 and thereby reduce potency.Example 13, with a terminal cyano group, retains some activity (MIC=3.1μM) due to the favorable interactions with the hydrophobic acyl chainpocket, whereas the terminal methoxy group of Example 14 (MIC>100 μM)may introduce clashes between lone pairs on the ether oxygen andproximal hydrophobic side chains (Gly200, Ile202, Pro206, Phe239).Interestingly, Example 11 and Example 30, with an n-pentyl sulfonamide,offer increased hydrophobic interactions, presenting an explanation forthe 2-fold increase in potency over DG167.

KasA is a valid drug discovery target within M. tuberculosis with apotential to rapidly kill M. tuberculosis and perhaps shorten treatmentin clinical TB, especially when used in combination with INK.

Example 55

The following illustrate representative pharmaceutical dosage forms,containing a compound of formula I (‘Compound X’), for therapeutic orprophylactic use in humans.

(i) Tablet 1 mg/tablet Compound X= 100.0 Lactose 77.5 Povidone 15.0Croscarmellose sodium 12.0 Microcrystalline cellulose 92.5 Magnesiumstearate 3.0 300.0

(ii) Tablet 2 mg/tablet Compound X= 20.0 Microcrystalline cellulose410.0 Starch 50.0 Sodium starch glycolate 15.0 Magnesium stearate 5.0500.0

(iii) Capsule mg/capsule Compound X= 10.0 Colloidal silicon dioxide 1.5Lactose 465.5 Pregelatinized starch 120.0 Magnesium stearate 3.0 600.0

(iv) Injection 1 (1 mg/ml) mg/ml Compound X = (free acid form) 1.0Dibasic sodium phosphate 12.0 Monobasic sodium phosphate 0.7 Sodiumchloride 4.5 1.0N Sodium hydroxide solution q.s. (pH adjustment to7.0-7.5) Water for injection q.s. ad 1 mL

(v) Injection 2 (10 mg/ml) mg/ml Compound X = (free acid form) 10.0Monobasic sodium phosphate 0.3 Dibasic sodium phosphate 1.1 Polyethyleneglycol 400 200.0 1.0N Sodium hydroxide solution q.s. (pH adjustment to7.0-7.5) Water for injection q.s. ad 1 mL

(vi) Aerosol mg/can Compound X= 20.0 Oleic acid 10.0Trichloromonofluoromethane 5,000.0 Dichlorodifluoromethane 10,000.0Dichlorotetrafluoroethane 5,000.0The above formulations may be obtained by conventional procedures wellknown in the pharmaceutical art.

All publications, patents, and patent documents are incorporated byreference herein, as though individually incorporated by reference. Theinvention has been described with reference to various specific andpreferred embodiments and techniques. However, it should be understoodthat many variations and modifications may be made while remainingwithin the spirit and scope of the invention.

What is claimed is:
 1. A method for treating a bacterial infection in ananimal comprising administering to the animal a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein: R¹ is H,(C₁-C₄)alkyl, phenyl, or benzyl; R² is H, halo, or (C₁-C₄)alkyl that isoptionally substituted with one or more halo; R³ is H and R⁴ is—N(R^(a))SO₂R^(c), —N(R^(a))C(═S)N(R^(a))R^(c), —N(R^(a))C(═O)R^(c),—N(R^(a))C(═O)OR^(c), —N(R^(a))R^(d), or —N(R^(a))C(═O)N(R^(a))R^(c); orR³ is —N(R^(a))SO₂R^(c), —N(R^(a))C(═S)N(R^(a))R^(c),—N(R^(a))C(═O)R^(c), —N(R^(a))C(═O)OR^(c), —N(R^(a))R^(d), or—N(R^(a))C(═O)N(R^(a))R^(c) and R⁴ is H; R⁵ is H, (C₁-C₄)alkyl, or halo;each R^(a) is independently H or (C₁-C₄)alkyl; R^(c) is(C₃-C₆)cycloalkyl, piperidinyl, or (C₂-C₆)alkyl, wherein any(C₃-C₆)cycloalkyl and (C₂-C₆)alkyl is optionally substituted with one ormore groups independently selected from the group consisting of halo,(C₃-C₆)cycloalkyl, phenyl, (C₁-C₄)alkoxy, trifluoromethyl, and cyano;and R^(d) is (C₃-C₆)cycloalkyl, or (C₂-C₆)alkyl, wherein any(C₃-C₆)cycloalkyl and (C₂-C₆)alkyl is optionally substituted with one ormore groups independently selected from the group consisting of halo,(C₃-C₆)cycloalkyl, phenyl, (C₁-C₄)alkoxy, trifluoromethyl, and cyano;provided the compound is not:


2. The method of claim 1, wherein the compound or pharmaceuticallyacceptable salt is a compound of formula (Ie):

wherein R² is H, halo, or (C₁-C₄)alkyl or a pharmaceutically acceptablesalt thereof.
 3. The method of claim 1, wherein R¹ is H, methyl, or CD3.4. The method of claim 1, wherein R² is H or methyl.
 5. The method ofclaim 1, R³ is H and R⁴ is —N(R^(a))SO₂R^(c).
 6. The method of claim 1,R³ is —N(R^(a))SO₂R^(c) and R⁴ is H.
 7. The method of claim 1, R³ is Hand R⁴ is —N(R^(a))C(═S)N(R^(a))R^(c).
 8. The method of claim 1, whereinR³ is —N(R^(a))C(═S)N(R^(a))R^(c) and R⁴ is H.
 9. The method of claim 1,wherein: R¹ is H, or (C₁-C₄)alkyl; R² is H, (C₁-C₄)alkyl, or halo; R³ isH and R⁴ is —N(R^(a))SO₂R^(c) or —N(R^(a))C(═S)N(R^(a))R^(c); or R³ is—N(R^(a))SO₂C or —N(R^(a))C(═S)N(R^(a))R^(c) and R⁴ is H; each R^(a) isindependently H or (C₁-C₄)alkyl; and R^(c) is (C₃-C₆)cycloalkyl, or(C₂-C₆)alkyl, wherein any (C₃-C₆)cycloalkyl and (C₂-C₆)alkyl isoptionally substituted with one or more groups independently selectedfrom the group consisting of halo, and cyano.
 10. The method of claim 1,wherein: R¹ is H; R² is H, halo, or (C₁-C₄)alkyl that is optionallysubstituted with one or more halo; R³ is H and R⁴ is —N(R^(a))SO₂R^(c),R⁵ is H, (C₁-C₄)alkyl, or halo; each R^(a) is independently H or(C₁-C₄)alkyl; and R^(c) is (C₃-C₆)cycloalkyl, or (C₂-C₆)alkyl, whereinany (C₃-C₆)cycloalkyl and (C₂-C₆)alkyl is optionally substituted withone or more groups independently selected from the group consisting ofhalo, (C₃-C₆)cycloalkyl, phenyl, (C₁-C₄)alkoxy, trifluoromethyl, andcyano.
 11. The method of claim 10, wherein the compound orpharmaceutically acceptable salt is a compound of formula (Ie):

wherein R² is H, halo, or (C₁-C₄)alkyl or a pharmaceutically acceptablesalt thereof.
 12. The method of claim 10, wherein R² is H or methyl. 13.The method of claim 10, wherein R¹ is H; R² is H, (C₁-C₄)alkyl, or halo;R³ is H and R⁴ is —N(R^(a))SO₂R^(c); each R^(a) is independently H or(C₁-C₄)alkyl; and R^(c) is (C₃-C₆)cycloalkyl, or (C₂-C₆)alkyl, whereinany (C₃-C₆)cycloalkyl and (C₂-C₆)alkyl is optionally substituted withone or more groups independently selected from the group consisting ofhalo, and cyano.
 14. The method of claim 10, wherein R^(c) is(C₃-C₆)alkyl that is optionally substituted with one or more groupsindependently selected from the group consisting of halo and cyano. 15.The method of claim 10, wherein the compound or pharmaceuticallyacceptable salt is selected from the group consisting of:

and pharmaceutically acceptable salts thereof.
 16. The method of claim 1that further comprises administering another compound that is aninhibitor of KasA to the animal.
 17. The method of claim 1 that furthercomprises administering another antibacterial drug to the animal. 18.The method of claim 17, wherein the other antibacterial drug is anantitubercular drug.
 19. The method of claim 17, wherein the otherantibacterial drug is isoniazid.
 20. A method for treating a bacterialinfection in an animal comprising administering isoniazid and a compoundof formula:

to the animal.